Methods and kits for isolation and analysis of a chromatin region

ABSTRACT

The present invention encompasses methods of identifying proteins and protein modifications of proteins specifically associated with a chromatin.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/744,844, filed Jun. 19, 2015, which claims the benefit of U.S.provisional application No. 62/014,428, filed Jun. 19, 2014, and U.S.application Ser. No. 14/744,844 is a continuation-in-part of U.S.application Ser. No. 14/081,812, filed Nov. 15, 2013, which claims thepriority of U.S. provisional application No. 61/726,936, filed Nov. 15,2012, and U.S. provisional application No. 61/875,969, filed Sep. 10,2013, each of which is hereby incorporated by reference in its entirety.

GOVERNMENTAL RIGHTS

This invention was made with government support under R01DA025755,F32GM093614, P20RR015569, P20RR016460, U54RR020839, and UL1TR000039awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The invention describes methods of identifying proteins andpost-translational modification of proteins specifically associated witha chromatin region.

REFERENCE TO SEQUENCE LISTING

A paper copy of the sequence listing and a computer readable form of thesame sequence listing are appended below and herein incorporated byreference. The information recorded in computer readable form isidentical to the written sequence listing, according to 37 C.F.R.1.821(f).

BACKGROUND OF THE INVENTION

It has long been appreciated that chromatin-associated proteins andepigenetic factors play central roles in gene regulation. Mis-regulationof chromatin structure and post-translational modification of histones(PTMs) is linked to cancer and other epigenetic diseases. The field ofepigenomics has been transformed by chromatin immunoprecipitationapproaches that provide for the localization of a defined protein orpost-translationally modified protein to specific chromosomal sites.However, the hierarchy of chromatin-templated events orchestrating theformation and inheritance of different epigenetic states remains poorlyunderstood at a molecular level; there are no current methodologies thatallow for determination of all proteins present at a defined, smallregion of chromatin. Chromatin immunoprecipitation (ChIP) assays haveallowed better understanding of genome-wide distribution of proteins andhistone modifications within a genome at the nucleosome level. However,ChIP assays are largely confined to examining singular histone PTMs orproteins rather than simultaneous profiling of multiple targets, theinability to determine the co-occupancy of particular histone PTMs, andthat ChIP is reliant on the previous identification of the moleculartarget. Other chromatin immunoprecipitation methodologies do not providea mechanism for determining the specificity of protein interactions, ordo not enrich for a small integrated genomic locus and cannot detectprotein contamination in purified material. Therefore, there is a needfor methods that allow for determination of all proteins and proteinposttranslational modifications specifically associated at a defined,small region of chromatin.

SUMMARY OF THE INVENTION

In an aspect, the present invention encompasses a method of identifyingproteins, including proteins comprising posttranslational modifications,specifically associated with a target chromatin in a cell. The methodcomprises: (a) providing a first cell sample comprising nucleic acidbinding proteins and the target chromatin and a tag, wherein the targetchromatin is tagged by contacting the target chromatin with a tagcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the tag comprises an affinity handle,and a second cell sample comprising nucleic acid binding proteins andthe target chromatin, wherein the target chromatin is not tagged bycontacting the target chromatin with a non-functional tag that is notcapable of specifically recognizing and binding one or more portions ofthe target chromatin and wherein the non-functional tag comprises anaffinity handle; (b) isolating the affinity handle from each cell samplein (a) wherein affinity handle isolated from the first cell sampleconsists of affinity handle bound to tagged target chromatin bound tospecifically associated nucleic acid binding proteins and affinityhandle bound to non-specifically associated nucleic acid bindingproteins and affinity handle isolated from the second cell sampleconsists of affinity handle bound to non-specifically associated nucleicacid binding proteins, wherein isolating the affinity handle enrichesfor the tagged target chromatin; (c) identifying bound proteins from(b); and (d) determining the amount of each bound protein in each cellsample from (b), wherein bound proteins that are enriched in the firstcell sample as compared to the second cell sample are specificallyassociated with the tagged chromatin in the first cell sample.

BRIEF DESCRIPTION OF THE FIGURES

The application file contains at least one drawing executed in color.Copies of this patent application publication with color drawing(s) willbe provided by the Office upon request and payment of the necessary fee.

FIG. 1A and FIG. 1B depict the chromatin affinity purification with massspectrometry method. (FIG. 1A) The chromatin affinity purification withmass spectrometry (ChAP-MS) approach provides for the specificenrichment of a given chromosome section and identification ofspecifically associated proteins and post-translational modifications. ALexA DNA affinity handle was engineered just upstream of the GAL1 startcodon in S. cerevisiae. Strains containing the LexA DNA binding site anda plasmid expressing LexA-PrA protein affinity handle were cultured inglucose or galactose to provide transcriptional repression oractivation, respectively, and subjected to in vivo chemical crosslinkingto trap protein interactions. Following shearing of the chromatin to˜1,000 bp, LexA-PrA was affinity purified on IgG-coated Dynabeads andcoenriched proteins/post-translational modifications were identified byhigh-resolution mass spectrometry. (FIG. 1B) To control fornonspecifically enriched proteins, a strain lacking the LexA DNA bindingsite, but containing the LexA-PrA plasmid, was cultured isotopicallyheavy (¹³C₆ ¹⁵N₂-lysine) in glucose or galactose and mixed equally withthe corresponding isotopically light culture containing the LexA DNAbinding site prior to cell lysis. Following affinity purification (AP)and mass spectrometric analysis, nonspecifically enriched proteins wereidentified as a 1:1 ratio of light to heavy lysine-containing peptides,while proteins specifically enriched with the chromosome section wereidentified with a higher level of isotopically light lysine-containingpeptides.

FIG. 2A and FIG. 2B depict a plot, a Western blot image and a plotshowing DNA affinity handle for purification of a specific chromosomesection. (FIG. 2A) S. cerevisiae strain LEXA::GAL1 pLexA-PrA was createdby insertion of a LEXA DNA binding site upstream of the GAL1 start codonvia homologous recombination. The pLexA-PrA plasmid was introduced intothis strain and the constitutive expression of the LexA-PrA fusionprotein was confirmed by western blotting for PrA. (FIG. 2B)Introduction of the LEXA DNA binding site does not impede GAL1transcription. cDNA from wild-type or LEXA::GAL1 pLexA-PrA strains grownin glucose or galactose was used as a template for real time PCRanalysis of GAL1 versus ACT1 gene transcription. Error bars are the SEof triplicate analyses.

FIG. 3A, FIG. 3B and FIG. 3C depict plots and a diagram showingefficiency of GAL1 chromatin purification. (FIG. 3A) The effect ofbuffer stringency on purification of LexA-PrA with associated chromatinwas evaluated with ChIP. Strain LEXA::GAL1 pLexA-PrA was subjected toChIP using the following buffer with the reagents indicated on thegraph: 20 mM HEPES (pH 7.4), 0.1% Tween 20, and 2 mM MgCl₂. Enrichmentof GAL1 DNA relative to ACT1 DNA was monitored by real-time PCR. (FIG.3B) ChIP was used to measure the specificity of enrichment of LexA-PrAbound chromatin. Enrichment was monitored by real-time PCR with primersets at the indicated chromosomal locations. (FIG. 3C) GAL1 chromatin isenriched in both glucose and galactose growth conditions. The relativeefficiency of GAL1 enrichment was monitored by real-time PCR withprimers targeted to the “0” position in panel (FIG. 3B) and to ACT1. TheSE is indicated.

FIG. 4A, FIG. 4B, FIG. 4C and FIG. 4D depict an image of an SDS-PAGE geland mass spectra showing ChAP-MS analysis of GAL1 chromatin. (FIG. 4A)Enrichment of GAL1 chromatin under transcriptionally repressive glucoseand active galactose growth conditions. Strain LEXA::GAL1 pLexA-PrA wasgrown in either glucose or galactose and subjected to affinitypurification of GAL1 chromatin via LexA-PrA as detailed in FIG. 1.Addition of an equivalent amount of isotopically heavy (¹³C₆¹⁵N₂-lysine) cells lacking the LexA DNA binding site provided for theidentification of proteins specifically enriched with GAL1 chromatin.Proteins coenriching with LexA-PrA were resolved by SDS-PAGE andvisualized by Coomassie-staining. Each gel lane was sliced into 2 mmsections. Gel slices were treated with trypsin and resulting peptideswere analyzed by high-resolution mass spectrometry. (FIG. 4B, FIG. 4C,FIG. 4D) Representative high-resolution mass spectra from proteins andhistone post-translational modifications identified from thepurification of transcriptionally active GAL1 chromatin. (FIG. 4B)Spt16; (FIG. 4C) H3K14ac; (FIG. 4D) Rpl3 (ribosomal).

FIG. 5 depicts a plot showing proteins and histone post-translationalmodifications enriched with GAL1 chromatin. Proteins and histonepost-translational modifications identified from the ChAP-MS analysis ofGAL1 chromatin in the transcriptionally active galactose and repressiveglucose growth conditions are listed in accordance to their percentisotopically light. Proteins or post-translational modifications wereconsidered specifically enriched with GAL1 chromatin if the percentisotopically light was 2 SDs from the nonspecific baseline establishedby the average of contaminant ribosomal proteins. Other proteins shownto be specifically enriched, but not correlated to gene transcription,are averaged together and listed individually in Table 4 and Table 5.The number of proteins averaged is shown in parentheses. The SD isindicated.

FIG. 6 depicts a plot showing the validation of proteins and histonepost-translational modifications on GAL1 chromatin. ChIP was targeted toGal3-TAP, Spt16-TAP, Rpb2-TAP, H3K14ac, and H3K36me3 undertranscriptionally active galactose and repressive glucose growthconditions. ChIP to general H3 was used as a nucleosome occupancycontrol for each histone post-translational modification ChIP.Enrichment of the 5′ end of GAL1 DNA relative to ACT1 DNA was monitoredby real-time PCR. The SE is indicated.

FIG. 7A, FIG. 7B, FIG. 7C, FIG. 7D, FIG. 7E, FIG. 7F and FIG. 7G depictdiagrams and graphs showing that TAL proteins can specifically enrichnative chromatin sections. (FIG. 7A) Schematic overview of TAL-ChAP-MStechnology. (FIG. 7B) A unique DNA sequence in the promoter region ofGAL1 was used to design a specific binding TAL protein that contained aPrA affinity tag. (FIG. 7C) A pTAL-PrA plasmid was introduced into S.cerevisiae cells, and the constitutive expression of the TAL-PrA fusionprotein was confirmed by western blotting for PrA. (FIG. 7D) Expressionof TAL-PrA does not impede galactose-induced GAL1 transcription. cDNAfrom wild-type yeast and wild-type with a plasmid expressing PrA-taggedTAL (+pTAL-PrA) grown in glucose (Glu) or galactose (Gal) was used as atemplate for real time PCR analysis of GAL1 versus ACT1 genetranscription. Error bars are the standard deviation. (FIG. 7E, FIG. 7F,FIG. 7G) TAL-PrA specifically binds and enriches chromatin at thepromoter of transcriptionally active GAL1. ChIP was performed to thePrA-tag in wild-type cells containing the TAL-PrA (+pTAL-PrA, light graybars) and in wild-type control (dark gray bars). The efficiency of GAL1enrichment relative to ACT1 was monitored by real-time PCR with primerstargeted to the TAL binding site (‘0’) and to DNA sequences 2000 by up-and downstream (FIG. 7E). The standard deviation is indicated. (FIG. 7F)Under transcriptionally active conditions (galactose), TAL-PrAspecifically enriched chromatin from the GAL1 promoter region relativeto sequences 2 kb up- and downstream. (FIG. 7G) The TAL-PrA protein didnot show enrichment of the GAL1 promoter chromatin undertranscriptionally repressive glucose growth conditions.

FIG. 8A, FIG. 8B and FIG. 8C depict an image of an SDS-PAGE gel andgraphs showing TAL-ChAP-MS analysis of GAL1 promoter chromatin fromcells grown its galactose. (FIG. 8A) Proteins co-purifying with TAL-PrAtargeted to the promoter region of GAL1 (+pTAL-PrA lane) and proteinsnon-specifically associating with the IgG-coated Dynabeads (wild-typelane) were resolved by SDS-PAGE/Coomassie-staining and identified byhigh-resolution mass spectrometry. (FIG. 8B) Proteins found bylabel-free proteomic analysis to be enriched by >2-fold withtranscriptionally active GAL1 promoter chromatin are plotted inaccordance to their ranked level of enrichment divided by the totalnumber of enriched proteins (N). Highlighted are the top 10% of proteins(>15-fold enrichment) and histone PTMs enriched with GAL1 promoterchromatin. (FIG. 8C) ChIP was targeted to Spt16-TAP, Rpb2-TAP, Gal3-TAPand H3K14ac under transcriptionally active galactose (light gray bars)and repressive glucose (dark gray bars) growth conditions, ChIP togeneral H3 was used as a nucleosome occupancy control for H3K14ac ChIP.Enrichment adjacent to the TAL binding site in the promoter of GAL1relative to ACT1 was monitored by real-time qPCR. The standard error isindicated.

FIG. 9 depicts an illustration of the CRISPR-ChAP-MS approach.PrA-tagged Cas9 bound to gRNA is targeted to a specific region ofchromatin. Following chemical cross-linking, the chromatin is sheared toapproximately 1 kb in size and subjected to affinity isolation withIgG-coated beads. Isolated chromatin containing PrA-tagged Cas9/gRNA isthen analyzed with high resolution mass spectrometry to identifyspecifically associated proteins and histone posttranslationalmodifications.

FIG. 10A, FIG. 10B and FIG. 10C depict a Western blot and graphs showinga PrA-tagged Cas9/gRNA complex can specifically enrich a small chromatinsection. (FIG. 10A) Using Western-blotting to the PrA-tag, similarexpression of PrA-Cas9 was shown in both glucose andgalactose-containing media. Western-blotting to histone H4 was used as aloading control. S. cerevisiae were transformed with either a plasmidexpressing PrA-tagged Cas9 (pPrA-Cas9) and/or a plasmid expressing gRNAspecific to a sequence in the promoter of GAL1 (pgRNA-GAL1). (FIG. 10B)Real-time reverse transcription PCR showed similar galactose-inducedtranscription of the GAL1 gene relative to ACT1 in cells expressingPrA-Cas9±gRNA-GAL1. Transcript levels of GAL1 are reported as a ratio ofdetection in galactose relative to glucose-containing media. (FIG. 10C)PrA-Cas9/gRNA complex specifically enriched GAL1 promoter chromatinunder transcriptionally active conditions. Using ChIP to the PrA-tag onCas9, enrichment at each indicated target relative to actin was measuredin cells containing the PrA-Cas9/gRNA complex in comparison to thosewith only the PrA-Cas9. The genomic targets were: GAL1 for the genomictarget of the gRNA-GAL1, 2000 base-pairs up- and downstream of thegRNA-GAL1 target, and four off-target (OT) sites for thePrA-Cas9/gRNA-GAL1 complex containing varying levels of sequencesimilarity to the gRNA-GAL1 target (±protospacer-activation motif (PAMmotif)). Error bars are standard error from triplicate analyses. (*)indicates significant (p<0.05) enrichment from galactose growthsrelative to glucose.

FIG. 11A and FIG. 11B depict a SDS-PAGE gel and a graph showingCRISPR-ChAP-MS analysis of transcriptionally active promoter chromatin.(FIG. 11A) Chromatin was affinity purified on IgG-beads from cells grownin galactose-containing media that expressed PrA-Cas9 as a control andcells that expressed PrA-Cas9/gRNA targeted to the promoter region ofGAL1. Co-enriched proteins were resolved by SDS-PAGE and identified withhigh resolution mass spectrometry. Label-free proteomics was used todetermine whether a protein or histone PTM was specifically enrichedwith the promoter chromatin. (FIG. 11B) ChIP to PrA-tagged versions ofthe proteins or to the histone PTM (normalized for nucleosome occupancy)purified with the promoter chromatin was used to validate enrichment atthe GAL1 promoter relative to ACT1. Cells were grown in either glucoseor galactose-containing media.

DETAILED DESCRIPTION OF THE INVENTION

A method of isolating and identifying proteins associated with a targetregion of chromatin in a cell has been discovered. The method may alsobe used to identify post-translational modifications (PTMs) of proteinsassociated with a target chromatin in a cell. Advantageously, the methodmay be used to determine whether the association of the identifiedproteins with a chromatin in a cell is specific or non-specific. As usedherein, “specifically associated” or “specific association” of a proteinwith a target chromatin refers to any protein in a cell that normallyassociates with a chromatin in a cell. In addition, and as illustratedin the examples, the method may be used to determine the role ofproteins and post-translational modifications (PTMs) of proteins inchromatin function, including regulatory mechanisms of transcription,and the role of epigenomic factors in controlling chromatin function.

I. Method of ChAP-MS

In some aspects, the invention provides methods of isolating andidentifying proteins specifically associated with a target chromatin. Asdescribed in Example 1 and FIG. 1, a method of the invention comprisesisolating a target chromatin from a cell. As used herein, a “targetchromatin” refers to a specific chromatin or a chromatin fragment thatmay be used in an application of the invention. According to the method,isolating the target chromatin isolates nucleic acid sequences andproteins, including proteins comprising posttranslational modifications,associated with the target chromatin. The proteins and posttranslationalmodifications of proteins associated with the target chromatin may thenbe identified, and a determination of which of the identified proteinsand posttranslational modifications of proteins associated with a targetchromatin isolated from a cell are specifically or non-specificallyassociated with the target chromatin is made.

To determine which of the identified proteins and posttranslationalmodifications of proteins associated with a target chromatin isolatedfrom a cell are specifically or non-specifically associated with thetarget chromatin, a method of the invention provides two cell samples,or lysates derived from two cell samples, comprising the targetchromatin, wherein proteins in one cell sample, but not both of the cellsamples are metabolically labeled. Typically, the two cell samples aregrown identically. In addition, the target chromatin in one of the cellsamples or an extract from one of the cell samples is tagged. The twocell samples, or lysates derived from the cell samples of the inventionare combined. The tagged target chromatin is isolated in the presence ofthe other cell sample or an extract from the other cell sample.Therefore, if a target chromatin of the invention is tagged in theunlabeled cell sample, proteins specifically associated with the taggedchromatin are unlabeled, and will be isolated in the presence of labeledproteins from the labeled cell sample. Alternatively, if a targetchromatin of the invention is tagged in the labeled cell sample, theproteins associated with the tagged chromatin are labeled, and will beisolated in the presence of unlabeled proteins from the unlabeled cellsample.

As such, determining if a certain identified protein associated with thetarget chromatin is labeled, unlabeled, or a combination of labeled andunlabeled may determine if the protein was specifically associated witha target chromatin of the invention. If an identified protein comprisesa mixture of labeled and unlabeled proteins, then that protein becameassociated with a target chromatin during the chromatin isolationprocedure, and association of that protein with the target chromatin isnot specific. If a target chromatin of the invention is isolated fromthe unlabeled cell sample, only unlabeled identified proteins associatedwith the target chromatin are specifically associated with the targetchromatin. Alternatively, if a target chromatin of the invention isisolated from the labeled cell sample, only labeled identified proteinsassociated with the target chromatin are specifically associated withthe target chromatin.

In some embodiments, a tagged target chromatin of the invention isisolated from an unlabeled cell sample, and unlabeled proteinsassociated with the target chromatin are specifically associated withthe target chromatin. In other embodiments, a tagged target chromatin ofthe invention is isolated from a labeled cell sample, and labeledproteins associated with the target chromatin are specificallyassociated with the target chromatin.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. A cell may be anarchaebacterium, a eubacterium, or a eukaryotic cell. For instance, acell of the invention may be a methanogen, a halophile or athermoacidophile archaeabacterium, a gram positive, a gram negative, acyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell,a moss cell, a plant cell, an animal cell, or a protist cell.

In some embodiments, a cell of the invention is a cell from an animal. Acell from an animal cell may be a cell from an embryo, a juvenile, or anadult. Suitable animals include vertebrates such as mammals, birds,reptiles, amphibians, and fish. Examples of suitable mammals includewithout limit rodents, companion animals, livestock, and primates.Non-limiting examples of rodents include mice, rats, hamsters, gerbils,and guinea pigs. Suitable companion animals include but are not limitedto cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples oflivestock include horses, goats, sheep, swine, cattle, llamas, andalpacas. Suitable primates include but are not limited to humans,capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins,spider monkeys, squirrel monkeys, and vervet monkeys. Non-limitingexamples of birds include chickens, turkeys, ducks, and geese. In someembodiments, a cell is a cell from a human.

In some embodiments, a cell may be from a model organism commonly usedin laboratory research. For instance, a cell of the invention may be anE. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasmagenitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonasfluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyosteliumdiscoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or aThalassiosira pseudonana protist cell; an Ashbya gossypii, anAspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, aNeurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune,a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; anArabidopsis thaliana, a Selaginella moellendorffii, a Brachypodiumdistachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicagotruncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotianabenthamiana plant cell; a Physcomitrella patens moss; an Amphimedonqueenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia seaslug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegansnematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, aDrosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, aLoligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsisleidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleuradioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyalehawaiensis crustacean, a Platynereis dumerilii marine polychaetousannelid, a Pristionchus pacificus roundworm, a Schmidtea mediterraneafreshwater planarian, a Stomatogastric ganglion of various arthropodspecies, a Strongylocentrotus purpuratus sea urchin, a Symsagittiferaroscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplaxadhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, aGuinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medakafish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugupufferfish, an African clawed frog, or a Zebrafish. In exemplaryembodiments, a cell is a Saccharomyces cerevisiae yeast cell. Inparticularly exemplary embodiments, a cell is a Saccharomyces cerevisiaeW303a yeast cell.

A cell of the invention may be derived from a tissue or from a cell linegrown in tissue culture. A cell line may be adherent or non-adherent, ora cell line may be grown under conditions that encourage adherent,non-adherent or organotypic growth using standard techniques known toindividuals skilled in the art. Cell lines and methods of culturing celllines are known in the art. Non-limiting examples of cell lines commonlycultured in a laboratory may include HeLa, a cell line from the NationalCancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap(prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer),PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloidleukemia), U87 (glioblastoma), SHSY5Y Human neuroblastoma cells, Saos-2cells (bone cancer), Vero, GH3 (pituitary tumor), PC12(pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells,Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), orXenopus A6 kidney epithelial cells.

A cell of the invention may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section (I) above, two cell samples, or lysates derivedfrom two cell samples are combined, and a tagged target chromatin of theinvention is isolated from the combined cells or combined cell lysates.Typically, cells in two cell samples of the invention are from the sametype of cells or they may be derived from the same type of cells. Forinstance, cells may comprise a heterologous nucleic acid in a targetchromatin, and may also comprise a heterologous protein expressed in acell of the invention. The heterologous nucleic acid in a targetchromatin may be used for tagging a chromatin of the invention, and theheterologous protein expressed in a cell may be used for tagging atarget chromatin as described in Section I(d). In some embodiments,cells in two cell samples of the invention are from the same type ofcells. In other embodiments, cells in the first cell sample are derivedfrom the same cell type as cells in the second cell sample.

Two cell samples of the invention may be from the same genus, species,variety or strain of cells. In preferred embodiments, two cell samplesof the invention are Saccharomyces cerevisiae yeast cells or derivativesof Saccharomyces cerevisiae yeast cells. In exemplary embodiments, twocell samples of the invention are Saccharomyces cerevisiae W303a yeastcells or derivatives of Saccharomyces cerevisiae W303a yeast cells. Inexemplary embodiments, two cell samples of the invention are derivativesof Saccharomyces cerevisiae W303a yeast cells comprising the lexAbinding site upstream of the GAL1 transcription start site, whereinprotein A is expressed in one of the cell samples of derivedSaccharomyces cerevisiae W303a yeast cells.

According to the invention, a metabolically labeled cell sample and anunlabeled cell sample are combined to generate a combined cell sample,or lysates derived from the two cell samples are combined to generate acombined cell lysate. Cell samples may be combined in a weight to weight(w/w) ratio of about 1:100 to about 100:1, about 1:50 to about 50:1,about 1:25 to about 25:1, preferably about 1:10 to about 10:1, and morepreferably about 1:5 to about 5:1. In preferred embodiments, cellsamples are combined in a w/w ratio of about 1:5 to about 5:1, about 1:2to about 2:1, about 1:1.5 to about 1.5:1, or about 1:1. In exemplaryembodiments, cell samples are combined in a w/w ratio of about 1:1. Ifcell lysates derived from two cell samples of the invention arecombined, lysates derived from cell ratios described herein arecombined. Individuals of ordinary skill in the art will recognize thatratios of cell samples or lysates derived from cell samples describedherein may be subject to statistical confidence limits of actual cellweight. For instance, the ratio may be based on 85, 90, 95% or moreconfidence limits on cell weight.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, if a cell of the invention is Saccharomyces cerevisiae, about5×10¹⁰ to about 5×10¹², more preferably, about 1×10¹¹ to about 1×10¹²cells may be used in a cell sample. In some embodiments, about about1×10¹¹ to about 1×10¹² Saccharomyces cerevisiae cells are used in a cellsample.

Two cell samples of the invention are typically grown identically.Identically grown cell samples minimizes potential structural orfunctional differences at a target chromatin present in both cellsamples. As used herein, “grown identically” refers to cultured cellsamples grown using similar culture condition, or cells from a tissueharvested using identical harvesting techniques. As described below, thetwo cell samples of the invention are grown identically in a manner thatallows the metabolic labeling of proteins in one of the cell samples.For instance, the two cell samples of the invention are grownidentically, except that one of the cell samples may be grown in thepresence of a labeled amino acid as described in the examples, togenerate a cell sample with metabolically labeled proteins.

Proteins in a cell sample are metabolically labeled. Methods ofmetabolically labeling proteins in a cell are known in the art and maycomprise culturing a cell in the presence of at least one labeledanalogue of a biomolecule that is metabolized by a cell of theinvention. When the labeled analog of a biomolecule is supplied to cellsin culture instead of the unlabeled biomolecule, the labeled biomoleculeis incorporated into all newly synthesized proteins. After a number ofcell divisions, each instance of this particular labeled biomoleculewill be replaced by its labeled analog. Since there is hardly anychemical difference between the labeled biomolecule and the unlabeledbiomolecule, the cells behave exactly like the control cell populationgrown in the presence of unlabeled biomolecule. As such, up to 100% ofthe particular biomolecule in a cell may be labeled. In someembodiments, up to 10, 20, 30, 40, 50, 60, 70, 80, 90 or up to 100% ofthe particular biomolecule in a cell is labeled. In preferredembodiments, up to 50, 60, 70, 80, 90 or up to 100%, and more preferablyup to 90 or up to 100% of the particular biomolecule in a cell islabeled. In preferred embodiments, up to 100% of the particularbiomolecule in a cell is labeled.

A cell may be labeled by culturing a cell in the presence of one or morethan one labeled biomolecule. For instance, a cell may be cultured inthe presence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more labeledbiomolecules. In some embodiments, a cell may be cultured in thepresence of 1, 2, 3, 4, or 5 labeled biomolecules. In other embodiments,a cell may be cultured in the presence of 5, 6, 7, 8, 9, or 10 labeledbiomolecules. In preferred embodiments, a cell may be cultured in thepresence of 1 or 2 labeled biomolecules.

Non-limiting examples of a biomolecule that may be labeled and ismetabolized by a cell of the invention may include an amino acid, anucleic acid, a carbohydrate or a labeled molecule that may beincorporated into an amino acid, a nucleic acid, or a carbohydrate.Non-limiting examples of a labeled molecule that may be incorporatedinto an amino acid, a nucleic acid, a carbohydrate may include labeledammonium sulfate, and labeled ammonium chloride. A labeled biomoleculemay be a component of a cell culture medium such as a food source, e.g.,glucose, sera or cell extracts. In some embodiments, a labeledbiomolecule that is metabolized by a cell of the invention is a labelednucleic acid. In other embodiments, a labeled biomolecule that ismetabolized by a cell of the invention is a labeled carbohydrate such as[¹³C]glucose.

In preferred embodiments, a biomolecule that is metabolized by a cell ofthe invention is a labeled amino acid. In general, a labeled amino acidof the invention may be a labeled L-amino acid, a labeled D-amino acidor a mixture thereof. In preferred embodiments, a labeled amino acids isa labeled L-amino acids. A labeled amino acid may be a free amino acidor an amino acid salt. A labeled amino acid may also be in the form ofintact protein or peptide, provided that the protein or peptidecomprises a labeled amino acid of the invention. In some preferredembodiments, a labeled amino acid that may be used for metabolicallylabeling a cell of the invention may be a labeled L-Lysine, L-Arginine,L-Methionine, L-Tyrosine, or combinations thereof.

A labeled biomolecule may be labeled using a heavy isotope of one ormore atoms of the biomolecule. Non limiting examples of a heavy isotopeof one or more atoms of a biomolecule may include heavy hydrogen,carbon, nitrogen, phosphorous, oxygen, or sulfur. A labeled biomoleculemay be about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1718, 19 or 20 Da or more heavier than an unlabeled biomolecule. In someembodiments, a labeled biomolecule is about 1, 2, 3, 4, or 5 Da heavierthan an unlabeled biomolecule. In other embodiments, a labeledbiomolecule is about 5, 6, 7, 8, 9, or 10 Da heavier than an unlabeledbiomolecule. In yet other embodiments, a labeled biomolecule is about10, 11, 12, 13, 14, or 15 Da heavier than an unlabeled biomolecule. Inadditional embodiments, a labeled biomolecule is about 15, 16, 17 18, 19or 20 Da heavier than an unlabeled biomolecule. In preferredembodiments, a labeled biomolecule is about 4, 5, 6, 7, 8, 9, or 10 Daheavier than an unlabeled biomolecule.

In preferred embodiments, a labeled biomolecule is a labeled amino acidthat may be used for metabolically labeling a cell of the invention maybe a heavy analog of L-Lysine, L-Arginine, L-Methionine, L-Tyrosine, orcombinations thereof. Non limiting examples of heavy analogs ofL-Lysine, L-Arginine, L-Methionine, L-Tyrosine may include,[¹³C₆]-L-Lysine, [¹³C₆, ¹⁵N₂]-L-Lysine, [¹³C₆, ¹⁵N₂, D9]-L-Lysine,[¹⁵N₂, D9]-L-Lysine, [4,4,5,5-D4]-L-Lysine, [¹⁵N₂]-L-Lysine, [¹³C₆,¹⁵N₂]-L-Lysine, [¹³C₆]-L-Arginine, [U-¹³C₆, ¹⁵N₄]-L-Arginine, [U-¹³C₆,¹⁵N₄, D7]-L-Arginine, [¹⁵N₄, D7]-L-Arginine, [¹⁵N₄]-L-Arginine, [¹³C₆,¹⁵N₄]-L-Arginine, [1-13C, methyl-D3]-L-Methionine, [¹³C₉; 9Da]-L-Tyrosine, [¹⁵N]-L-Tyrosine, and [¹³C₉, ¹⁵N]-L-Tyrosine. In anexemplary embodiment, a labeled amino acid used to metabolically label acell of the invention is [¹³C6, ¹⁵N4]-L-Arginine.

(b) Chromatin

A method of the invention comprises identification of a protein andpost-translational modification of a protein associated with a targetchromatin. Generally, chromatin refers to the combination of nucleicacids and proteins in the nucleus of a eukaryotic cell. However, it iscontemplated that the term “chromatin” may also refer to the combinationof any nucleic acid sequence and proteins associated with the nucleicacid sequence in any cell.

A chromatin of the invention may comprise single stranded nucleic acid,double stranded nucleic acid, or a combination thereof. In someembodiments, a chromatin comprises single stranded nucleic acid. Inother embodiments, a chromatin comprises a combination of singlestranded and double stranded nucleic acids. In yet other embodiments, achromatin comprises double stranded nucleic acid.

A chromatin of the invention may comprise a ribonucleic acid (RNA), adeoxyribonucleic acid (DNA), or a combination of RNA and DNA. In someembodiments, a chromatin of the invention comprises a combination of aRNA sequence and proteins associated with the RNA sequence in a cell.Non-limiting examples of RNA sequences may include mRNA, and non-codingRNA such as tRNA, rRNA, snoRNAs, microRNAs, siRNAs, piRNAs and the longnoncoding RNA (IncRNA). In preferred embodiments, a chromatin of theinvention comprises a combination of a DNA sequence and proteinsassociated with the DNA sequence in a cell. In other preferredembodiments, a chromatin of the invention comprises a combination of RNAand DNA sequences, and proteins associated with the RNA and DNA sequencein a cell. Non limiting examples of chromatin that may comprise acombination of RNA and DNA may include genomic DNA undergoingtranscription, or genomic DNA comprising non-coding RNA such as IncRNA.

A chromatin of the invention may be genomic chromatin such as, chromatinfrom a chromosome of a cell, or chromatin from an organelle in the cell.Alternatively, a chromatin may be chromatin from an extrachromosomalnucleic acid sequence. In some embodiments, a chromatin of the inventionis chromatin from an organelle in the cell. Non-limiting examples of achromatin from an organelle may include mitochondrial nucleic acidsequence in plant and animal cells, and a chloroplast nucleic acidsequence in plant cells. In some embodiments, a nucleic acid sequence ofthe invention is a mitochondrial nucleic acid sequence. In otherembodiments, a nucleic acid sequence of the invention is a chloroplastnucleic acid sequence.

In some embodiments, a chromatin of the invention is chromatin from anextrachromosomal nucleic acid sequence. The term “extrachromosomal,” asused herein, refers to any nucleic acid sequence not contained withinthe cell's genomic nucleic acid sequence. An extrachromosomal nucleicacid sequence may comprise some sequences that are identical or similarto genomic sequences in the cell, however, an extrachromosomal nucleicacid sequence as used herein does not integrate with genomic sequencesof the cell. Non-limiting examples of an extrachromosomal nucleic acidsequence may include a plasmid, a virus, a cosmid, a phasmid, and aplasmid.

In some preferred embodiments, a chromatin of the invention is genomicchromatin. In exemplary embodiments, a chromatin of the invention isgenomic chromatin of a eukaryotic cell. A eukaryotic cell of theinvention may be as described in Section I(a) above.

Primary functions of genomic chromatin of a eukaryotic cell may be DNApackaging into a smaller volume to fit in the cell, strengthening of theDNA to allow mitosis, prevent DNA damage, and to control gene expressionand DNA replication. As described above, genomic chromatin of aeukaryotic cell may comprise DNA sequences and a plurality ofDNA-binding proteins as well as certain RNA sequences, assembled intohigher order structural or functional regions. As used herein, a“structural or functional feature of a chromatin”, refers to a chromatinfeature characterized by, or encoding, a function such as a regulatoryfunction of a promoter, terminator, translation initiation, enhancer,etc., or a structural feature such as heterochromatin, euchromatin, anucleosome, a telomere, or a centromere. A physical feature of a nucleicacid sequence may comprise a functional role and vice versa. Asdescribed below, a chromatin of the invention may be a chromatinfragment, and as such may comprise a fragment of a physical orfunctional feature of a chromatin, or no physical or functional featuresor known physical or functional features.

The primary protein components of genomic eukaryotic chromatin arehistones that compact the DNA into a nucleosome. The nucleosomecomprises an octet of histone proteins around which is wound a stretchof double stranded DNA sequence of about 150 to about 250 bp in length.Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1may act to link adjacent nucleosomes together into a higher orderstructure. Histones are subject to post translational which may affecttheir function in regulating chromatin function. Such modifications mayinclude methylation, citrullination, acetylation, phosphorylation,SUMOylation, ubiquitination, and ADP-ribosylation.

Many further polypeptides and protein complexes interact with thenucleosome and the histones to regulate chromatin function. A“polypeptide complex” as used herein, is intended to describe proteinsand polypeptides that assemble together to form a unitary association offactors. The members of a polypeptide complex may interact with eachother via non-covalent or covalent bonds. Typically members of apolypeptide complex will cooperate to enable binding either to a nucleicacid sequence or to polypeptides and proteins already associated with orbound to a nucleic acid sequence in chromatin. Chromatin associatedpolypeptide complexes may comprise a plurality of proteins and/orpolypeptides which each serve to interact with other polypeptides thatmay be permanently associated with the complex or which may associatetransiently, dependent upon cellular conditions and position within thecell cycle. Hence, particular polypeptide complexes may vary in theirconstituent members at different stages of development, in response tovarying physiological conditions or as a factor of the cell cycle. Byway of example, in animals, polypeptide complexes with known chromatinremodelling activities include Polycomb group gene silencing complexesas well as Trithorax group gene activating complexes.

Additionally, a protein associated with a chromatin of the invention maybe a protein normally expressed in a cell, or may be an exogenousheterologous protein expressed in a cell. In some embodiments, a proteinassociated with a chromatin of the invention is a protein normallyexpressed in a cell. In other embodiments, a protein associated with achromatin of the invention is a protein not normally expressed in acell.

A chromatin of the invention may be an intact and complete chromatinfrom the cell, or may be a fragment of a chromatin in a cell. In someembodiments, a chromatin of the invention is an intact chromatinisolated from a cell. For instance, a chromatin of the invention may bea plasmid, a cosmid, or a phage chromatin or a complete organellarchromatin. In preferred embodiments, a chromatin of the invention is afragment of a chromatin from a cell. In exemplary embodiments, achromatin of the invention is a fragment of a genomic chromatin from acell.

When a chromatin of the invention is a fragment of a chromatin in acell, any method of fragmenting a chromatin known in the art may beused. Such methods may include physical methods of fragmenting achromatin, or enzymatic digestion of a nucleic acid sequence of achromatin. In some embodiments, a fragment of a chromatin may begenerated using enzymatic digestion of a nucleic acid sequence inchromatin. Non-limiting examples of enzymatic digestion may includerandom or sequence specific enzymatic digestion using restrictionenzymes, nucleases, combinations of restriction enzymes and nucleases,or combinations of nicking and other nucleases such as NEBNext™fragmentase, which comprises a nicking enzyme that randomly generatesnicks in double stranded DNA and another enzyme that cuts the strandopposite to the generated nicks.

In other embodiments, a fragment of a chromatin may be generated using aphysical method of fragmenting a chromatin. Non-limiting examples ofphysical fragmenting methods that may be used to fragment a chromatin ofthe invention may include nebulization, sonication, and hydrodynamicshearing. In some embodiments, a fragment of a chromatin may begenerated using nebulization. In other embodiments, a fragment of achromatin may be generated using hydrodynamic shearing. In preferredembodiments, a fragment of a chromatin may be generated usingsonication. During sonication, a sample comprising chromatin issubjected to ultrasonic waves, whose vibrations produce gaseouscavitations in the liquid that shear or break high molecular weightmolecules such as chromatin through resonance vibration. Sonicationmethods that may be used to generate a chromatin of the invention areknown in the art

A fragment of a chromatin of the invention may comprise a nucleic acidsequence fragment and may be about 10, 50, 100, 150, 200, 250, 300, 350,400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650,1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250,2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850,2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000bases long or more. In some embodiments, a chromatin of the inventionmay comprise a nucleic acid sequence fragment of about 10, 20, 30, 40,50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470,480, 490, or about 500 bases long. In other embodiments, a chromatin ofthe invention may comprise a nucleic acid sequence fragment of about500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630,640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, or about 1000 bases long. In yetother embodiments, a chromatin of the invention may comprise a nucleicacid sequence fragment of about 1000, 1010, 1020, 1030, 1040, 1050,1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170,1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290,1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410,1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 baseslong. In other embodiments, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1500, 1510, 1520, 1530, 1540,1550, 1560, 1570, 1580, 1590, 1600, 1610, 1620, 1630, 1640, 1650, 1660,1670, 1680, 1690, 1700, 1710, 1720, 1730, 1740, 1750, 1760, 1770, 1780,1790, 1800, 1810, 1820, 1830, 1840, 1850, 1860, 1870, 1880, 1890, 1900,1910, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, or about 2000bases long. In additional embodiments, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 2000, 2100, 2150,2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In otherembodiments, a chromatin of the invention may comprise a nucleic acidsequence fragment of about 2000, 2050, 2100, 2150, 2200, 2250, 2300,2350, 2400, 2450, or about 2500 bases long. In still other embodiments,a chromatin of the invention may comprise a nucleic acid sequencefragment of about 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900,2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 baseslong or more.

In some preferred embodiments, a chromatin fragment of the invention maycomprise a nucleic acid sequence fragment of about 550, 560, 570, 580,590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720,730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860,870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120,1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240,or about 1250 bases long. In a preferred embodiment, a chromatin of theinvention may comprise a nucleic acid sequence fragment of about 750,760, 770, 780, 790, 800, 810, 820, 830, 840, or about 850 bases long. Inanother preferred embodiment, a chromatin of the invention may comprisea nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, or about 1050 bases long.

In other preferred embodiments, a chromatin fragment of the inventionmay comprise a nucleic acid sequence fragment of about 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040,1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160,1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280,1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400,1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500bases long. In a preferred embodiment, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 950, 960, 970, 980,990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long. In anotherpreferred embodiment, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1200, 1210, 1220, 1230, 1240,1250, 1260, 1270, 1280, 1290, or about 1300 bases long.

As described in this section above, a chromatin of the invention maycomprise one or more nucleosomes. As such, a chromatin fragment of theinvention may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, or about 20 nucleosomes. In some embodiments, achromatin fragment of the invention may comprise about 1, 2, 3, 4, orabout 5 nucleosomes. In other embodiments, a chromatin fragment of theinvention may comprise about 5, 6, 7, 8, 9, or about 10 nucleosomes. Inyet other embodiments, a chromatin fragment of the invention maycomprise about 10, 11, 12, 13, 14, or about 15 nucleosomes. In otherembodiments, a chromatin fragment of the invention may comprise about15, 16, 17, 18, 19, or about 20 nucleosomes. In preferred embodiments, achromatin fragment of the invention may comprise about 4 nucleosomes. Inother preferred embodiments, a chromatin fragment of the invention maycomprise about 5 nucleosomes.

A target chromatin fragment of the invention may comprise a structuralor a functional feature of chromatin as described above, a fragment of aphysical or functional feature, or no physical or functional features orknown physical or functional features. In some embodiments, a targetchromatin fragment of the invention comprises a structural feature ofchromatin. In other embodiments, a target chromatin fragment of theinvention comprises no physical or functional features or known physicalor functional features. In yet other embodiments, a target chromatinfragment of the invention comprises a functional feature of chromatin.In exemplary embodiments, a functional feature of chromatin is apromoter. In particularly exemplary embodiments, a functional feature ofchromatin is a GAL1 promoter of Saccharomyces cerevisiae.

(c) Preparation of Cell Lysate

A target chromatin is isolated from a combined cell lysate. A combinedcell lysate comprises a lysate of two combined cell samples, or acombination of two cell lysates derived from two cell samples, wherein atarget chromatin is tagged in one of the cell samples. Irrespective ofwhether one cell sample or a combined cell sample is lysed, a skilledpractitioner of the art will appreciate that structural and functionalfeatures of a target chromatin must be preserved during cell lysis andisolation of the target chromatin. The association of proteins with atarget chromatin may be preserved during cell lysis and isolation of thetarget chromatin using methods known in the art for preserving a complexof proteins with a nucleic acid sequence. For instance, lysing of a celland isolation of a target chromatin may be performed under refrigerationor using cryogenic methods and buffer conditions capable of preservingassociation of proteins and nucleic acid sequences. In addition, acomplex of proteins with a nucleic acid may be preserved by crosslinkingprotein and nucleic acid complexes in a cell prior to lysing andisolating a chromatin. Crosslinking protein and nucleic acid complexesin a cell may also capture, or preserve, transient protein-protein andprotein-nucleic acid interactions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the chromatin.Crosslinking is the process of joining two or more molecules such as twoproteins or a protein and a nucleic acid molecule, by a covalent bond.Molecules may be crosslinked by irradiation with ultraviolet light, orby using chemical crosslinking reagents. Chemical crosslinking reagentscapable of crosslinking proteins and nucleic acids are known in the artand may include crosslinking reagents that target amines, sulfhydryls,carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctionalcrosslinking reagent, variable spacer arm length or zero-lengthcrosslinking reagents, cleavable or non-cleavable crosslinking reagents,and photoreactive crosslinking reagents. Non-limiting examples ofcrosslinking reagents that may be used to crosslink protein complexesand/or protein complexes and nucleic acids may include formaldehyde,glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, aphotoreactive amino acid such as photo-leucine or photo-methionine, andsuccinimidyl-diazirine. The degree of crosslinking can and will varydepending on the application of a method of the invention, and may beexperimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentcondition can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples.

(d) Chromatin Isolation

According to the invention, a tagged target chromatin is isolated from acombined cell lysate. As described in Sections I(a) and I(c) above, acombined cell lysate comprises a lysate of two combined cell samples, ora combination of two cell lysates derived from two cell samples, whereina target chromatin is tagged in one of the lysates, or one of the cellsamples. As such, a target chromatin is isolated from a cell lysatecomprising a combination of a tagged target chromatin and an untaggedtarget chromatin. The ratio of tagged target chromatin to untaggedtarget chromatin reflects the ratio at which the two cell samples or thelysates derived from the two cell sample are combined. In addition,proteins in one of the cell samples or lysate derived from one of thecell samples are metabolically labeled. Therefore, when a tagged targetchromatin is from a cell sample wherein proteins are metabolicallylabeled, a cell lysate of the invention comprises a combination of atagged target chromatin comprising metabolically labeled proteins, andan untagged target chromatin comprising unlabeled proteins. Conversely,when a tagged target chromatin is from a cell sample wherein proteinsare unlabeled, a cell lysate of the invention comprises a combination ofa tagged target chromatin comprising unlabeled proteins, and an untaggedtarget chromatin comprising labeled proteins.

A target chromatin may be isolated from a mixture of chromatins orchromatin fragments in a cell lysate as described in this section. Asused herein, a target nucleic acid sequence is said to be “isolated” or“purified” when it is substantially free of proteins not associated withthe target chromatin, nucleic acid sequences other than the nucleic acidsequences associated with the target chromatin, and other cell debrisand cell contents resulting from extraction and preparation of thetarget chromatin from a cell. A target chromatin of the presentinvention may be purified to homogeneity or other degrees of purity. Ingeneral, the level of purity of an isolated target chromatin can andwill vary depending on the cell type, the specific chromatin to beisolated, and the intended use of a target chromatin of the invention.The level of purity of an isolated target chromatin may be determinedusing methods known in the art. For instance, the level of purity of anisolated target chromatin may be determined by determining the level ofpurity of a nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell. Determining the level ofenrichment of a target chromatin, compared to a non-target chromatin ina cell may be as described in this section below.

A target chromatin of the invention may be isolated using methods knownin the art, such as electrophoresis, molecular, immunological andchromatographic techniques, ion exchange, hydrophobic, affinity, andreverse-phase HPLC chromatography, size exclusion chromatography,precipitation, dialysis, chromatofocusing, ultrafiltration anddiafiltration techniques, and combinations thereof. For general guidancein suitable purification techniques, see Scopes, R., ProteinPurification, Springer-Vertag, NY (1982).

In general, a method of the invention comprises isolating a targetchromatin by affinity purification, or affinity purification incombination with other methods of isolating chromatin described above.In a preferred embodiment, a method of the invention comprises isolatinga target chromatin by affinity purification. Non limiting examples ofaffinity purification techniques that may be used to isolate a targetchromatin of the invention may include affinity chromatography,immunoaffinity chromatography, size exclusion chromatography, andcombinations thereof. See, for example, Roe (ed), Protein PurificationTechniques: A Practical Approach, Oxford University Press, 2nd edition,2001.

In essence, affinity purification of a target chromatin may comprisetagging a target chromatin by contacting the target chromatin of theinvention with a tag capable of specifically recognizing and binding oneor more portions of a target chromatin. As used herein, “specificallyrecognizing” refers to a binding reaction between two separate moleculesthat is at least two times the background and more typically more than10 to 100 times the background molecular associations underphysiological conditions. As described in Section (I), two cell samples,or lysates derived from the cell samples of the invention are combined,and a target chromatin in one of the cell samples or an extract from oneof the cell samples is tagged. In addition, proteins in one cell sample,but not both of the cell samples are metabolically labeled. As such, atarget chromatin may be tagged in a cell or an extract from a cellwherein proteins are metabolically labeled, and proteins specificallyassociated with an isolated target chromatin are metabolically labeled.Alternatively, a target chromatin may be tagged in a cell or an extractfrom a cell wherein proteins are not metabolically labeled, and proteinsspecifically associated with an isolated target chromatin are notmetabolically labeled. In some embodiments, a target chromatin is taggedin a cell or an extract from a cell wherein proteins are metabolicallylabeled. In other embodiments, a target chromatin is tagged in a cell oran extract from a cell wherein proteins are metabolically labeled.

A tag may be capable of specifically recognizing and binding 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and bindingone component of a target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. In someembodiments, a tag is capable of specifically recognizing and binding aprotein associated with a target chromatin. In other embodiments, a tagis capable of specifically recognizing and binding a chromatinstructural or functional feature in a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and binding anucleic acid sequence associated with a target chromatin.

A nucleic acid sequence associated with a target chromatin that may bespecifically recognized and bound by a tag of the invention may be anucleic acid sequence normally found in a chromatin of a cell of theinvention. Alternatively, a nucleic acid sequence associated with atarget chromatin that may be specifically recognized and bound by a tagof the invention may be an exogenous nucleic acid sequence introducedinto a cell to facilitate tagging a target chromatin of the invention.In some embodiments, a nucleic acid sequence that may be recognized andbound by a tag is a nucleic acid sequence normally found in a chromatinof a cell of the invention. In other embodiments, a nucleic acidsequence that may be recognized and bound by a tag of the invention isan exogenous nucleic acid sequence introduced into a cell of theinvention to facilitate tagging a chromatin of the invention. Nonlimiting examples of an exogenous nucleic acid sequence introduced intoa cell to facilitate tagging a target chromatin of the invention may bethe lexA binding sequence, and the Lac operator. In a preferredembodiment, a heterologous nucleic acid sequence introduced into a cellto facilitate tagging a target nucleic acid sequence of the invention isthe lexA binding sequence. In an exemplary embodiment, a heterologousnucleic acid sequence introduced into a cell to facilitate tagging atarget nucleic acid sequence of the invention is the lexA bindingsequence immediately upstream of the transcription start site.

Individuals of ordinary skill in the art will recognize that anexogenous chromatin component introduced into a cell to facilitatetagging a target chromatin of the invention cannot and will not disrupta target chromatin, or a structural or functional feature of a targetchromatin. Methods of designing a chromatin component and a tag capableof binding the chromatin component that do not disrupt a chromatin ofthe invention may depend on the particular application of a method ofthe invention, and may be determined experimentally. For instance, if anapplication of a method of the invention comprises promoter function, atag may be designed to bind anywhere adjacent to the promoter, butwithout disrupting the promoter.

A tag of the invention may further comprise one or more affinityhandles. As used herein, the term “affinity handle” may refer to anyhandle that may be bound by a substrate for affinity purification, asdescribed below. A tag may comprise one or more than one affinityhandle. The inclusion of more than one affinity handle in a tag of theinvention may significantly increase the efficiency of affinitypurification for a low copy number chromatin target. As such, a tag mayfurther comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles.In a preferred embodiment, a tag of the invention comprises one affinityhandle.

Affinity handles may include any affinity handle for which a cognatebinding agent is readily available. An affinity handle may be anaptamer, an antibody, an antibody fragment, a double-stranded DNAsequence, modified nucleic acids and nucleic acid mimics such as peptidenucleic acids, locked nucleic acids, phosphorodiamidate morpholinooligomers (PMO), a ligand, a ligand fragment, a receptor, a receptorfragment, a polypeptide, a peptide, a coenzyme, a coregulator, anallosteric molecule, non-immunoglobulin scaffolds such as Affibodies,Anticalins, designed Ankyrin repeat proteins and others, an ion, or asmall molecule for which a cognate binding agent is readily available.The term “aptamer” refers to a polypeptide or a polynucleotide capableof binding to a target molecule at a specific region. It is generallyaccepted that an aptamer, which is specific in its binding to anypolypeptide, may be synthesized and/or identified by in vitro evolutionmethods. Non limiting examples of handles that may be suitable forisolating a chromatin may include biotin or a biotin analogue such asdesthiobiotin, digoxigenin, dinitrophenol or fluorescein, amacromolecule that binds to a nucleic acid or a nucleic acid bindingprotein such as the Lac repressor, a zinc finger protein, atranscription activator protein capable of binding a nucleic acid, or atranscription activator-like (TAL) protein, antigenic polypeptides suchas protein A, or peptide ‘tags’ such as polyhistidine, FLAG, HA and Myctags. In preferred embodiments, a tag of the invention comprises anantigenic polypeptide. In exemplary embodiments, a tag of the inventioncomprises the protein A antigenic polypeptide, or derivatives thereof.Protein A is capable of binding the lexA binding site, and comprises anaffinity handle capable of binding IgG. As such, protein A may be usedas an affinity purification tag for purifying a target chromatincomprising a lexA binding tag.

In some embodiments, a tag of the invention is a nucleic acid tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin isintroduced into a cell of the invention. In some embodiments, a tag ofthe invention is a nucleic acid tag capable of binding a nucleic acidsequence component of a chromatin, wherein the nucleic acid sequencecomponent of the chromatin is normally present in a cell of theinvention. Non-limiting examples of nucleic acid tags capable of bindinga nucleic acid sequence component of a chromatin include antisense RNAor DNA nucleic acid tags, and tags comprising modified nucleic acids andnucleic acid mimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO). In some embodiments, atag of the invention is a nucleic acid tag comprising lockednucleotides. For instance, a nucleic acid tag comprising lockednucleotides may be as described in US20110262908 or US20120040857, and apeptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS92:1901-1905, the disclosures of all of which are incorporated herein intheir entirety.

In some preferred embodiments, a tag of the invention is a protein tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin is anucleic acid sequence normally found in a chromatin of a cell of theinvention. Non limiting examples of a protein tag capable of binding anucleic acid sequence normally found in a chromatin of a cell may be anucleic acid binding protein such as protein A, the Lac repressor, azinc finger protein, a transcription activator protein capable ofbinding a nucleic acid, or a transcription activator-like (TAL) protein.In one embodiment, a tag of the invention is a transcription activatorprotein capable of binding a nucleic acid sequence normally found in achromatin of a cell of the invention. In another embodiment, a tag ofthe invention is a zinc finger protein capable of binding a nucleic acidsequence normally found in a chromatin of a cell of the invention. Inyet another embodiment, a tag of the invention is a transcriptionactivator-like (TAL) protein capable of binding a nucleic acid sequencenormally found in a chromatin of a cell of the invention.

A nucleic acid binding protein tag of the invention may be a wild typenucleic acid binding protein capable of binding a nucleic acid sequencenormally found in a target chromatin. Alternatively, a nucleic acidbinding protein tag of the invention may be engineered to have bindingspecificity for a nucleic acid sequence component normally found in atarget chromatin of the invention. Individuals of ordinary skill in theart will recognize that nucleic acid binding proteins such as zincfinger proteins, transcription activator proteins, and transcriptionactivator-like (TAL) proteins may be engineered to have novel nucleicacid binding specificity compared to naturally-occurring forms of theproteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, andU.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, thedisclosures of which are incorporated by reference herein in theirentireties. In some embodiments, a nucleic acid binding protein tag ofthe invention is a wild type nucleic acid binding protein capable ofbinding a nucleic acid sequence normally found in a target chromatin. Inother embodiments, a nucleic acid binding protein tag of the inventionis a nucleic acid binding protein engineered to have binding specificityfor a nucleic acid sequence component of a target chromatin of theinvention. In a preferred embodiment, a nucleic acid binding protein tagof the invention is a zinc finger protein engineered to have bindingspecificity for a nucleic acid sequence component of a target chromatinof the invention. In another preferred embodiment, a nucleic acidbinding protein tag of the invention is a TAL protein engineered to havebinding specificity for a nucleic acid sequence component of a targetchromatin of the invention.

In other preferred embodiments, a tag of the invention is a protein tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin is anexogenous nucleic acid sequence introduced into a cell of the invention.In exemplary embodiments, a tag of the invention is a protein A tagcapable of binding the lexA exogenous nucleic acid sequence introducedin a cell of the invention. In an exemplary embodiment, a tag of theinvention is a protein A tag capable of binding the lexA exogenousnucleic acid sequence introduced upstream of the transcriptional startsite of the GAL1 promoter of a S. cereviseae cell as described in theexamples.

A target chromatin may be contacted with a tag at any time during amethod of the invention leading to isolation of target chromatin. Forinstance, a target chromatin may be contacted with a protein tag duringcell culture by expressing the protein tag in a cell of the invention.Alternatively, a target chromatin may be contacted with a tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin.

In some embodiments, a target chromatin is contacted with a tag aftercell culture but before cell lysis. As such, a tag may be introducedinto a cell before cell lysis. Methods of introducing a tag into a cellof the invention can and will vary depending on the type of cell, thetag, and the application of a method of the invention. For instance, anucleic acid tag may be electroporated into a cell after culture. Inother embodiments, a target chromatin is contacted with a tag after celllysis. In such an embodiment, a tag may be added to the cell lysate as arecombinant protein. The recombinant protein may be expressed, isolatedand purified via methods standard in the art for protein purification.In yet other embodiments, a target chromatin is contacted with a tagafter cell lysis and chromatin fragmentation. In preferred embodiments,a target chromatin is contacted with a tag during cell culture byexpressing the tag in a cell of the invention during cell culture. Inexemplary embodiments, a target chromatin comprises the lexA bindingsite, and the lexA binding site is contacted with a protein A tag duringcell culture by expressing the protein A in a cell of the inventionduring cell culture. In an exemplary embodiment, a target chromatincomprises the lexA binding site, and the lexA binding site is contactedwith a protein A tag during cell culture by expressing the protein A ina yeast cell of the invention during cell culture as described in theexamples.

A target chromatin contacted and bound by a tag as described above maybe isolated using an affinity handle of the tag. The term “isolated”,may be used herein to describe a purified preparation of a targetchromatin that is enriched for the target chromatin, but wherein thetarget chromatin is not necessarily in a pure form. That is, an isolatedtarget chromatin is not necessarily 100% pure, but may be about 10%,20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated targetchromatin may be enriched for the target chromatin, relative to achromatin in the lysed preparation that was not contacted by a tag ofthe invention. An isolated target chromatin may be enriched by 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is notcontacted by a tag of the invention. In some embodiments, an isolatedtarget chromatin is enriched by 2, 3, 4, or 5 fold relative to achromatin that was not contacted by a tag of the invention. In otherembodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9,or 10 fold relative to a chromatin that was not contacted by a tag ofthe invention. In an exemplary embodiment, an isolated target chromatinis enriched 4, 5, or 6 fold relative to a chromatin that was notcontacted by a tag of the invention.

A target chromatin contacted and bound by a tag as described above maybe isolated using any affinity purification method known in the art. Inshort, a tagged target chromatin is bound to a substrate capable ofbinding the affinity handle. The substrate comprising a bound targetchromatin may then be washed to remove non-target chromatin and othercell debris, and the target chromatin may be released from substrate.Methods of affinity purification of material comprising an affinityhandle are known in the art and may include binding the affinity handleto a substrate capable of binding the affinity handle. The substrate maybe a gel matrix such as gel beads, the surface of a container, or achip. The tagged target chromatin bound to the substrate may then bepurified. Methods of purifying tagged molecules are known in the art andwill vary depending on the target molecule, the tag, and the substrate.For instance, if the tag is a protein A tag bound to a lexA binding sitein a target chromatin, the target chromatin may be bound to a magneticbead substrate comprising IgG, and purified using a magnet.

(e) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated target chromatin areextracted from the isolated target chromatin. Methods of extractingproteins from chromatin are generally known in the art of proteinbiochemistry. Generally, any extraction protocol suitable for isolatingproteins and known to those of skill in the art may be used. Extractedproteins may also be further purified before protein identification. Forinstance, protein extracts may be further purified by differentialprecipitation, differential solubilization, ultracentrifugation, usingchromatographic methods such as size exclusion chromatography,hydrophobic interaction chromatography, ion exchange chromatography,affinity chromatography, metal binding, immunoaffinity chromatography,HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In apreferred embodiment, extracted proteins are further purified usingSDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

As described above, proteins isolated with a chromatin of the inventionmay be labeled, unlabeled or a combination of labeled and unlabeledproteins. As described in Section I(d), if a target chromatin is taggedin a cell or an extract from a cell wherein proteins are metabolicallylabeled, proteins specifically associated with an isolated targetchromatin are metabolically labeled, whereas unlabeled proteins, orproteins comprising a combination of labeled and unlabeled proteins arenot specifically associated with the target chromatin. Alternatively, ifa target chromatin may be tagged in a cell or an extract from a cellwherein proteins are not metabolically labeled, proteins specificallyassociated with an isolated target chromatin are metabolically labeled,whereas unlabeled proteins, or proteins comprising a combination oflabeled and unlabeled proteins are not specifically associated with thetarget chromatin.

When an isolated and identified protein is a combination of labeled andunlabeled protein, the ratio of labeled to unlabeled protein may reflecta ratio at which a metabolically labeled cell sample and an unlabeledcell sample are combined to generate a combined cell sample, or lysatesderived from the two cell samples are combined to generate a combinedcell lysate. For instance, if a metabolically labeled cell sample and anunlabeled cell sample, or lysates derived from the two cell samples, arecombined at a ratio of 1:1, the ratio of labeled to unlabeled isolatedprotein may be 1:1.

However, since the ratio of labeled to unlabeled isolated proteindepends on the rate of exchange of the identified protein duringextraction and processing of a cell sample, a ratio of labeled tounlabeled isolated protein may differ from the ratio at which ametabolically labeled cell sample and an unlabeled cell sample arecombined to generate a combined cell sample, or lysates derived from thetwo cell samples are combined to generate a combined cell lysate. Forexample, if a metabolically labeled cell sample and an unlabeled cellsample, or lysates derived from the two cell samples, are combined at aratio of 1:1, a ratio of labeled to unlabeled isolated protein maydeviate from a ratio of 1:1. As such, a ratio of labeled to unlabeledisolated protein may be compared to a baseline for non-specificallyassociated proteins. For instance, a baseline for non-specificallyassociated proteins may be a ratio of labeled to unlabeled of one ormore proteins in a combined lysate, wherein the one or more proteins arenot associated with a chromatin. Non-limiting examples of proteins notassociated with a chromatin may include enzymes required for metabolism,receptors, and ribosomal proteins. In preferred embodiments, proteinsnot associated with a chromatin are ribosomal proteins, and a baselinefor non-specifically associated proteins is a ratio of a labeled tounlabeled ribosomal protein, or an average of ratios of labeled tounlabeled ribosomal proteins. In a preferred embodiment, proteins notassociated with a chromatin are 20 ribosomal proteins, and a baselinefor non-specifically associated proteins is an average of ratios of the20 labeled to unlabeled ribosomal proteins.

Isolated proteins with a ratio of labeled to unlabeled isolated proteinmay be specifically associated with a chromatin if the ratio of labeledto unlabeled isolated protein is significantly different from a baselineratio. A significantly different ratio may be a ratio of labeled tounlabeled isolated protein greater than about 1, 2, 3, 4, 5, or morestandard deviations than a baseline ratio. In some embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, ormore standard deviations than a baseline ratio. In other embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.5, 2, or about 2.5 standarddeviations than a baseline ratio. In preferred embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6,1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9 or about 3standard deviations than a baseline ratio. In exemplary embodiments, asignificantly different ratio is a ratio of labeled to unlabeledisolated protein greater than about 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1,2.2, 2.3, 2.4, or about 2.5 standard deviations than a baseline ratio.

Methods of determining if a protein or a protein fragment is labeled canand will vary depending on the type of label. For instance, if a proteinis labeled using a tag, labeling may be determined using methodsdesigned to detect the tag. For example, determining if a proteincomprising a his-tag is tagged, untagged, or a combination of tagged anduntagged may be by detecting the proteins comprising the his tag. If aprotein is labeled using a radioactive isotope, labeling may bedetermined by determining the degree of radioactivity of isolatedproteins or protein fragments. Alternatively, if a protein is labeledusing a heavy isotope, MS analysis may be used to determine if a proteinor a protein fragment is labeled or unlabeled. Advantageously, when aprotein is labeled using a heavy isotope, MS analysis may be used toidentify a protein or a protein fragment as described above, and toderive the MS data to determine if a protein or a protein fragment islabeled, unlabeled, or a combination of labeled and unlabeled protein orprotein fragment.

In preferred embodiments, a protein is labeled using a heavy isotope,and MS analysis is used to identify a protein or a protein fragment, andto determine if a protein or a protein fragment is labeled, unlabeled,or a combination of labeled and unlabeled protein or protein fragment.Methods of deriving MS data to determine if a protein or a proteinfragment is labeled, unlabeled, or a combination of labeled andunlabeled protein or protein fragment are known in the art, and mayinclude using known computational techniques to distill MS data such asMascot Distiller, Rosetta Elucidator, and MaxQuant. In some embodiments,MS data is derived using Rosetta Elucidator. In other embodiments, MSdata is derived using MaxQuant. In preferred embodiments, MS data isderived using Mascot Distiller.

II. Method of TAL-ChAP-MS

In another aspect, the invention provides a method of isolating andidentifying proteins specifically associated with a target chromatinusing the TAL protein as described in Example 4 and FIG. 7. TheTAL-ChAP-MS approach achieves high resolution and specificity by usingthe genomic targeting ability of the TALEN system for local epiproteomeisolation and analysis. To alleviate genomic engineering for affinityenrichment of chromatin sections, a specific TAL-protein is designedwith specificity for a target chromatin. This second-generationtechnology provides quantitative identification of specifically boundproteins and histone PTMs to a native chromatin region using label-freequantitative mass spectrometry.

To determine which of the identified proteins and posttranslationalmodifications of proteins associated with a target chromatin isolatedfrom a cell are specifically or non-specifically associated with thetarget chromatin, a method of high-resolution mass spectrometry coupledwith label-free proteomics was used. One with skill in the art willappreciate that label-free quantitative proteomics methods include thefollowing fundamental steps: (i) sample preparation including proteinextraction, reduction, alkylation, and digestion; (ii) sample separationby liquid chromatography (LC or LC/LC) and analysis by MS/MS; (iii) dataanalysis including peptide/protein identification, quantification, andstatistical analysis. A method of the invention provides two cellsamples, or lysates derived from two cell samples, comprising the targetchromatin, wherein the target chromatin in one cell sample, but not bothof the cell samples is tagged. With label-free quantitiative methods,each sample is separately prepared, then subjected to individualLC-MS/MS or LC/LC-MS/MS runs. As reviewed in Zhu et al., J BiomedBiotechnol 2010, and incorporated by reference herein, proteinquantification is generally based on two categories of measurements. Inthe first are the measurements of ion intensity changes such as peptidepeak areas or peak heights in chromatography. The second is based onspectral counting of identified proteins after MS/MS analysis. Peptidepeak intensity or spectral count is measured for individual LC-MS/MS orLC/LC-MS/MS runs and changes in protein abundance are calculated via adirect comparison between different analyses.

In the present invention, the method of spectral counting is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. As such, determining the abundance of anidentified protein in a tagged chromatin sample compared to the sameprotein in an untagged chromatin sample, may determine if the proteinwas specifically associated with the target chromatin of the invention.If a protein associated with a target chromatin is enriched in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, then the protein is specifically associated with the targetchromatin. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, thenassociation of that protein with the target chromatin is not specific.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. A cell may be anarchaebacterium, a eubacterium, or a eukaryotic cell. For instance, acell of the invention may be a methanogen, a halophile or athermoacidophile archaeabacterium, a gram positive, a gram negative, acyanobacterium, a spirochaete, or a firmicute bacterium, a fungal cell,a moss cell, a plant cell, an animal cell, or a protist cell.

In some embodiments, a cell of the invention is a cell from an animal. Acell from an animal cell may be a cell from an embryo, a juvenile, or anadult. Suitable animals include vertebrates such as mammals, birds,reptiles, amphibians, and fish. Examples of suitable mammals includewithout limit rodents, companion animals, livestock, and primates.Non-limiting examples of rodents include mice, rats, hamsters, gerbils,and guinea pigs. Suitable companion animals include but are not limitedto cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples oflivestock include horses, goats, sheep, swine, cattle, llamas, andalpacas. Suitable primates include but are not limited to humans,capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins,spider monkeys, squirrel monkeys, and vervet monkeys. Non-limitingexamples of birds include chickens, turkeys, ducks, and geese. In someembodiments, a cell is a cell from a human.

In some embodiments, a cell may be from a model organism commonly usedin laboratory research. For instance, a cell of the invention may be anE. coli, a Bacillus subtilis, a Caulobacter crescentus, a Mycoplasmagenitalium, an Aliivibrio fischeri, a Synechocystis, or a Pseudomonasfluorescens bacterial cell; a Chlamydomonas reinhardtii, a Dictyosteliumdiscoideum, a Tetrahymena thermophila, an Emiliania huxleyi, or aThalassiosira pseudonana protist cell; an Ashbya gossypii, anAspergillus nidulans, a Coprinus cinereus, a Cunninghamella elegans, aNeurospora crassa, a Saccharomyces cerevisiae, a Schizophyllum commune,a Schizosaccharomyces pombe, or an Ustilago maydis fungal cell; anArabidopsis thaliana, a Selaginella moellendorffii, a Brachypodiumdistachyon, a Lotus japonicus, a Lemna gibba, a Zea mays, a Medicagotruncatula, a Mimulus, a tobacco, a rice, a Populus, or a Nicotianabenthamiana plant cell; a Physcomitrella patens moss; an Amphimedonqueenslandica sponge, an Arbacia punctulata sea urchin, an Aplysia seaslug, a Branchiostoma floridae deuterostome, a Caenorhabditis elegansnematode, a Ciona intestinalis sea squirt, a Daphnia spp. crustacean, aDrosophila fruit fly, a Euprymna scolopes squid, a Hydra Cnidarian, aLoligo pealei squid, a Macrostomum lignano flatworm, a Mnemiopsisleidyicomb jelly, a Nematostella vectensis sea anemone, an Oikopleuradioica free-swimming tunicate, an Oscarella carmela sponge, a Parhyalehawaiensis crustacean, a Platynereis dumerilii marine polychaetousannelid, a Pristionchus pacificus roundworm, a Schmidtea mediterraneafreshwater planarian, a Stomatogastric ganglion of various arthropodspecies, a Strongylocentrotus purpuratus sea urchin, a Symsagittiferaroscoffensis flatworm, a Tribolium castaneum beetle, a Trichoplaxadhaerens Placozoa, a Tubifex tubifex oligochaeta, a laboratory mouse, aGuinea pig, a Chicken, a Cat, a Dog, a Hamster, a Lamprey, a Medakafish, a Rat, a Rhesus macaque, a Cotton rat, a Zebra finch, a Takifugupufferfish, an African clawed frog, or a Zebrafish. In exemplaryembodiments, a cell is a Saccharomyces cerevisiae yeast cell. Inparticularly exemplary embodiments, a cell is a Saccharomyces cerevisiaeW303a yeast cell.

A cell of the invention may be derived from a tissue or from a cell linegrown in tissue culture. A cell line may be adherent or non-adherent, ora cell line may be grown under conditions that encourage adherent,non-adherent or organotypic growth using standard techniques known toindividuals skilled in the art. Cell lines and methods of culturing celllines are known in the art. Non-limiting examples of cell lines commonlycultured in a laboratory may include HeLa, a cell line from the NationalCancer Institute's 60 cancer cell lines, DU145 (prostate cancer), Lncap(prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer),PC3 (prostate cancer), T47D (breast cancer), THP-1 (acute myeloidleukemia), U87 (glioblastoma), SHSY5Y Human neuroblastoma cells, Saos-2cells (bone cancer), Vero, GH3 (pituitary tumor), PC12(pheochromocytoma), MC3T3 (embryonic calvarium), Tobacco BY-2 cells,Zebrafish ZF4 and AB9 cells, Madin-Darby canine kidney (MDCK), orXenopus A6 kidney epithelial cells.

A cell of the invention may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section II above, two cell samples, or lysates derivedfrom two cell samples may be subjected to mass-spectrometry coupled withlabel-free proteomics, one sample of which contains a tagged targetchromatin of the invention. Typically, cells in two cell samples of theinvention are from the same type of cells or they may be derived fromthe same type of cells or derived from the same biological sample. Insome embodiments, cells may comprise a heterologous protein expressed ina cell of the invention. The heterologous protein expressed in a cellmay be used for tagging a target chromatin as described in SectionII(d). In some embodiments, cells in two cell samples of the inventionare from the same type of cells. In other embodiments, cells in thefirst cell sample are derived from the same cell type as cells in thesecond cell sample.

Two cell samples of the invention may be from the same genus, species,variety or strain of cells or from the same biological sample. In aspecific embodiment, two cell samples of the invention are Saccharomycescerevisiae yeast cells or derivatives of Saccharomyces cerevisiae yeastcells. In exemplary embodiments, two cell samples of the invention areSaccharomyces cerevisiae W303a yeast cells or derivatives ofSaccharomyces cerevisiae W303a yeast cells. In exemplary embodiments,two cell samples of the invention are derivatives of Saccharomycescerevisiae W303a yeast cells, wherein-protein A tagged transcriptionactivator-like (TAL) protein engineered to bind upstream of the GAL1transcription start site is expressed in one of the cell samples ofderived Saccharomyces cerevisiae W303a yeast cells.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, if a cell of the invention is Saccharomyces cerevisiae, about5×10¹⁰ to about 5×10¹², more preferably, about 1×10¹¹ to about 1×10¹²cells may be used in a cell sample. In some embodiments, about about1×10¹¹ to about 1×10¹² Saccharomyces cerevisiae cells are used in a cellsample.

Two cell samples of the invention are typically grown identically.Identically grown cell samples minimizes potential structural orfunctional differences at a target chromatin present in both cellsamples. As used herein, “grown identically” refers to cultured cellsamples grown using similar culture condition, or cells from a tissueharvested using identical harvesting techniques, or biological samplescollected, and optionally processed, via identical techniques.

(b) Chromatin

A method of the invention comprises identification of a protein andpost-translational modification of a protein associated with a targetchromatin. Generally, chromatin refers to the combination of nucleicacids and proteins in the nucleus of a eukaryotic cell. However, it iscontemplated that the term “chromatin” may also refer to the combinationof any nucleic acid sequence and proteins associated with the nucleicacid sequence in any cell.

Chromatin of the invention may be as described in Section I(b) above.

(c) Preparation of Cell Lysate

A target chromatin is isolated from a cell lysate derived from a cellsample, wherein a target chromatin is tagged in the cell sample. Themethod of isolating a target chromatin is also performed on a celllysate derived from a cell sample, wherein a target chromatin isuntagged in the cell sample. A skilled practitioner of the art willappreciate that structural and functional features of a target chromatinmust be preserved during cell lysis and isolation of the targetchromatin. The association of proteins with a target chromatin may bepreserved during cell lysis and isolation of the target chromatin usingmethods known in the art for preserving a complex of proteins with anucleic acid sequence. For instance, lysing of a cell and isolation of atarget chromatin may be performed under refrigeration or using cryogenicmethods and buffer conditions capable of preserving association ofproteins and nucleic acid sequences. In addition, a complex of proteinswith a nucleic acid may be preserved by crosslinking protein and nucleicacid complexes in a cell prior to lysing and isolating a chromatin.Crosslinking protein and nucleic acid complexes in a cell may alsocapture, or preserve, transient protein-protein and protein-nucleic acidinteractions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the chromatin.Crosslinking is the process of joining two or more molecules such as twoproteins or a protein and a nucleic acid molecule, by a covalent bond.Molecules may be crosslinked by irradiation with ultraviolet light, orby using chemical crosslinking reagents. Chemical crosslinking reagentscapable of crosslinking proteins and nucleic acids are known in the artand may include crosslinking reagents that target amines, sulfhydryls,carboxyls, carbonyls or hydroxyls; omobifunctional or heterobifunctionalcrosslinking reagent, variable spacer arm length or zero-lengthcrosslinking reagents, cleavable or non-cleavable crosslinking reagents,and photoreactive crosslinking reagents. Non-limiting examples ofcrosslinking reagents that may be used to crosslink protein complexesand/or protein complexes and nucleic acids may include formaldehyde,glutaraldehyde, disuccinimidyl glutarate, disuccinimidyl suberate, aphotoreactive amino acid such as photo-leucine or photo-methionine, andsuccinimidyl-diazirine. The degree of crosslinking can and will varydepending on the application of a method of the invention, and may beexperimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentconditions can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples.

(d) Chromatin Isolation

According to the invention, the method of isolating a target chromatinis performed on cell lysates derived from cell samples, wherein onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. As described in Sections II(a) and II(c) above, a cell lysatecomprises a lysate of a cell sample, wherein a target chromatin istagged in one of the lysates, or one of the cell samples. A cell lysatealso comprises a lysate of a cell sample, wherein a target chromatin isnot tagged in one of the lysates, or one of the cell samples.

A target chromatin may be isolated from a mixture of chromatins orchromatin fragments in a cell lysate as described in this section. Asused herein, a target nucleic acid sequence is said to be “isolated” or“purified” when it is substantially free of proteins not associated withthe target chromatin, nucleic acid sequences other than the nucleic acidsequences associated with the target chromatin, and other cell debrisand cell contents resulting from extraction and preparation of thetarget chromatin from a cell. A target chromatin of the presentinvention may be purified to homogeneity or other degrees of purity. Ingeneral, the level of purity of an isolated target chromatin can andwill vary depending on the cell type, the specific chromatin to beisolated, and the intended use of a target chromatin of the invention.The level of purity of an isolated target chromatin may be determinedusing methods known in the art. For instance, the level of purity of anisolated target chromatin may be determined by determining the level ofpurity of a nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell. Determining the level ofenrichment of a target chromatin, compared to a non-target chromatin ina cell may be as described in this section below.

A target chromatin of the invention may be isolated using methods knownin the art, such as electrophoresis, molecular, immunological andchromatographic techniques, ion exchange, hydrophobic, affinity, andreverse-phase HPLC chromatography, size exclusion chromatography,precipitation, dialysis, chromatofocusing, ultrafiltration anddiafiltration techniques, and combinations thereof. For general guidancein suitable purification techniques, see Scopes, R., ProteinPurification, Springer-Vertag, NY (1982).

In general, a method of the invention comprises isolating a targetchromatin by affinity purification, or affinity purification incombination with other methods of isolating chromatin described above.In a preferred embodiment, a method of the invention comprises isolatinga target chromatin by affinity purification. Non-limiting examples ofaffinity purification techniques that may be used to isolate a targetchromatin of the invention may include affinity chromatography,immunoaffinity chromatography, size exclusion chromatography, andcombinations thereof. See, for example, Roe (ed), Protein PurificationTechniques: A Practical Approach, Oxford University Press, 2nd edition,2001.

In essence, affinity purification of a target chromatin may comprisetagging a target chromatin by contacting the target chromatin of theinvention with a tag capable of specifically recognizing and binding oneor more portions of a target chromatin. As described in Section II, atarget chromatin from one cell sample, or lysate derived from the cellsample of the invention, but not both of the cell samples, is tagged.

A tag may be capable of specifically recognizing and binding 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 components of a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and bindingone component of a target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. In someembodiments, a tag is capable of specifically recognizing and binding aprotein associated with a target chromatin. In other embodiments, a tagis capable of specifically recognizing and binding a chromatinstructural or functional feature in a target chromatin. In preferredembodiments, a tag is capable of specifically recognizing and binding anucleic acid sequence associated with a target chromatin.

A nucleic acid sequence associated with a target chromatin that may bespecifically recognized and bound by a tag of the invention may be anucleic acid sequence normally found in a chromatin of a cell of theinvention. Individuals of ordinary skill in the art will recognize thata tag introduced into a cell to facilitate tagging a target chromatin ofthe invention cannot and will not disrupt a target chromatin, or astructural or functional feature of a target chromatin. Methods ofdesigning a tag capable of binding the chromatin component that do notdisrupt a chromatin of the invention may depend on the particularapplication of a method of the invention, and may be determinedexperimentally. For instance, if an application of a method of theinvention comprises promoter function, a tag may be designed to bindanywhere adjacent to the promoter, but without disrupting the promoter.

In some embodiments, a tag of the invention is a nucleic acid tagcapable of binding a nucleic acid sequence component of a chromatin,wherein the nucleic acid sequence component of the chromatin isintroduced into a cell of the invention. In some embodiments, a tag ofthe invention is a nucleic acid tag capable of binding a nucleic acidsequence component of a chromatin, wherein the nucleic acid sequencecomponent of the chromatin is normally present in a cell of theinvention. Non-limiting examples of nucleic acid tags capable of bindinga nucleic acid sequence component of a chromatin include antisense RNAor DNA nucleic acid tags, and tags comprising modified nucleic acids andnucleic acid mimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO). In some embodiments, atag of the invention is a nucleic acid tag comprising lockednucleotides. For instance, a nucleic acid tag comprising lockednucleotides may be as described in US20110262908 or US20120040857, and apeptide nucleic acid tag may be as described in Boffa et al. 1995 PNAS92:1901-1905, the disclosures of all of which are incorporated herein intheir entirety.

In specific embodiments, a tag of the invention is a protein tag capableof binding a nucleic acid sequence component of a chromatin, wherein thenucleic acid sequence component of the chromatin is a nucleic acidsequence normally found in a chromatin of a cell of the invention. Nonlimiting examples of a protein tag capable of binding a nucleic acidsequence normally found in a chromatin of a cell may be a nucleic acidbinding protein such as protein A, the Lac repressor, a zinc fingerprotein, a transcription activator protein capable of binding a nucleicacid, or a transcription activator-like (TAL) protein. In oneembodiment, a tag of the invention is a transcription activator proteincapable of binding a nucleic acid sequence normally found in a chromatinof a cell of the invention. In another embodiment, a tag of theinvention is a zinc finger protein capable of binding a nucleic acidsequence normally found in a chromatin of a cell of the invention. In anexemplary embodiment, a tag of the invention is transcriptionactivator-like (TAL) protein capable of binding a nucleic acid sequencenormally found in a chromatin of a cell of the invention.

A nucleic acid binding protein tag of the invention may be a wild typenucleic acid binding protein capable of binding a nucleic acid sequencenormally found in a target chromatin. Alternatively, a nucleic acidbinding protein tag of the invention may be engineered to specificallyrecognize a nucleic acid sequence component normally found in a targetchromatin of the invention. Individuals of ordinary skill in the artwill recognize that nucleic acid binding proteins such as zinc fingerproteins, transcription activator proteins, and transcriptionactivator-like (TAL) proteins may be engineered to have novel nucleicacid binding specificity compared to naturally-occurring forms of theproteins. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261, andU.S. Pate. Appl. Nos 20110239315, 20120110685, and 20120270273, thedisclosures of which are incorporated by reference herein in theirentireties. In some embodiments, a nucleic acid binding protein tag ofthe invention is a wild type nucleic acid binding protein capable ofbinding a nucleic acid sequence normally found in a target chromatin. Inother embodiments, a nucleic acid binding protein tag of the inventionis a nucleic acid binding protein engineered to specifically recognize anucleic acid sequence component of a target chromatin of the invention.In a preferred embodiment, a nucleic acid binding protein tag of theinvention is a zinc finger protein engineered to specifically recognizea nucleic acid sequence component of a target chromatin of theinvention. In an exemplary embodiment, a nucleic acid binding proteintag of the invention is a TAL protein engineered to specificallyrecognize a nucleic acid sequence component of a target chromatin of theinvention.

A tag of the invention may further comprise one or more affinityhandles. As used herein, the term “affinity handle” may refer to anyhandle that may be bound by a substrate for affinity purification, asdescribed below. A tag may comprise one or more than one affinityhandle. The inclusion of more than one affinity handle in a tag of theinvention may significantly increase the efficiency of affinitypurification for a low copy number chromatin target. As such, a tag mayfurther comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more affinity handles.In a preferred embodiment, a tag of the invention comprises one affinityhandle.

Affinity handles may include any affinity handle for which a cognatebinding agent is readily available. An affinity handle may be anaptamer, an antibody, an antibody fragment, a double-stranded DNAsequence, modified nucleic acids and nucleic acid mimics such as peptidenucleic acids, locked nucleic acids, phosphorodiamidate morpholinooligomers (PMO), a ligand, a ligand fragment, a receptor, a receptorfragment, a polypeptide, a peptide, a coenzyme, a coregulator, anallosteric molecule, non-immunoglobulin scaffolds such as Affibodies,Anticalins, designed Ankyrin repeat proteins and others, an ion, or asmall molecule for which a cognate binding agent is readily available.The term “aptamer” refers to a polypeptide or a polynucleotide capableof binding to a target molecule at a specific region. It is generallyaccepted that an aptamer, which is specific in its binding to anypolypeptide, may be synthesized and/or identified by in vitro evolutionmethods. Non limiting examples of handles that may be suitable forisolating a chromatin may include biotin or a biotin analogue such asdesthiobiotin, digoxigenin, dinitrophenol or fluorescein, antigenicpolypeptides such as protein A, or peptide ‘tags’ such as polyhistidine,FLAG, HA and Myc tags. In preferred embodiments, a tag of the inventioncomprises an antigenic polypeptide as an affinity handle. In otherpreferred embodiments, a tag of the invention comprises protein A orderivatives thereof as an affinity handle. In a specific embodiment, atag of the invention comprises protein A-tagged TAL protein. The TALprotein can be engineered to specifically recognize a nucleic acidsequence component of a target chromatin of the invention. As such, TALmay be used as an affinity purification tag for purifying a targetchromatin. Protein A comprises an affinity handle capable of bindingIgG. In exemplary embodiments, a tag of the invention comprises theprotein A tagged TAL protein engineered to bind upstream of the GAL1transcription start site.

A target chromatin may be contacted with a tag at any time during amethod of the invention leading to isolation of target chromatin. Forinstance, a target chromatin may be contacted with a protein tag duringcell culture by expressing the protein tag in a cell of the invention.Alternatively, a target chromatin may be contacted with a tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin. In such embodiments, a tag may be added to the cell cultureor cell lysate as a recombinant protein. The recombinant protein may beexpressed, isolated and purified via methods standard in the art forprotein purification.

In some embodiments, a target chromatin is contacted with a tag aftercell culture but before cell lysis. As such, a tag may be introducedinto a cell before cell lysis. Methods of introducing a tag into a cellof the invention can and will vary depending on the type of cell, thetag, and the application of a method of the invention. For instance, anucleic acid tag may be electroporated into a cell after culture. Inother embodiments, a target chromatin is contacted with a tag after celllysis. In such an embodiment, a tag may be added to the cell lysate as arecombinant protein. In yet other embodiments, a target chromatin iscontacted with a tag after cell lysis and chromatin fragmentation. Incertain embodiments, a target chromatin is contacted with a tag duringcell culture by expressing the tag in a cell of the invention duringcell culture. In exemplary embodiments, a target chromatin is contactedwith a protein A tagged TAL protein during cell culture by expressingthe protein A tagged TAL protein in a cell of the invention during cellculture.

A target chromatin contacted and bound by a tag as described above maybe isolated using an affinity handle of the tag. The term “isolated”,may be used herein to describe a purified preparation of a targetchromatin that is enriched for the target chromatin, but wherein thetarget chromatin is not necessarily in a pure form. That is, an isolatedtarget chromatin is not necessarily 100% pure, but may be about 10%,20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. An isolated targetchromatin may be enriched for the target chromatin, relative to achromatin in the lysed preparation that was not contacted by a tag ofthe invention. An isolated target chromatin may be enriched by 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 fold relative to a chromatin that is notcontacted by a tag of the invention. In some embodiments, an isolatedtarget chromatin is enriched by 2, 3, 4, or 5 fold relative to achromatin that was not contacted by a tag of the invention. In otherembodiments, an isolated target chromatin is enriched by 5, 6, 7, 8, 9,or 10 fold relative to a chromatin that was not contacted by a tag ofthe invention. In an exemplary embodiment, an isolated target chromatinis enriched 4, 5, or 6 fold relative to a chromatin that was notcontacted by a tag of the invention.

A target chromatin contacted and bound by a tag as described above maybe isolated using any affinity purification method known in the art. Inshort, a tagged target chromatin is bound to a substrate capable ofbinding the affinity handle. The substrate comprising a bound targetchromatin may then be washed to remove non-target chromatin and othercell debris, and the target chromatin may be released from substrate.Methods of affinity purification of material comprising an affinityhandle are known in the art and may include binding the affinity handleto a substrate capable of binding the affinity handle. The substrate maybe a gel matrix such as gel beads, the surface of a container, or achip. The tagged target chromatin bound to the substrate may then bepurified. Methods of purifying tagged molecules are known in the art andwill vary depending on the target molecule, the tag, and the substrate.For instance, if the tag is a TAL-protein A tag bound to a site in atarget chromatin, the target chromatin may be bound to a magnetic beadsubstrate comprising IgG, and purified using a magnet.

(e) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated target chromatin areextracted from the isolated target chromatin. Methods of extractingproteins from chromatin are generally known in the art of proteinbiochemistry. Generally, any extraction protocol suitable for isolatingproteins and known to those of skill in the art may be used. Extractedproteins may also be further purified before protein identification. Forinstance, protein extracts may be further purified by differentialprecipitation, differential solubilization, ultracentrifugation, usingchromatographic methods such as size exclusion chromatography,hydrophobic interaction chromatography, ion exchange chromatography,affinity chromatography, metal binding, immunoaffinity chromatography,HPLC, or gel electrophoriesis such as SDS-PAGE and QPNC-PAGE. In apreferred embodiment, extracted proteins are further purified usingSDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

In the present invention, the method of label-free proteomics is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. Label-free methods of quantifying proteins orprotein fragments are known in the art. In label-free quantitativeproteomics, each sample is separately prepared, then subjected toindividual methods of identifying proteins or protein fragments whichmay include LC-MS/MS or LC/LC-MS/MS. According to the invention, onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. Label-free protein quantification is generally based on twocategories of measurement. In the first are the measurements of ionintensity changes such as peptide peak areas or peak heights inchromatography. The second is based on the spectral counting ofidentified proteins after MS/MS analysis. Peptide peak intensity orspectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runsand changes in protein abundance are calculated via a direct comparisonbetween different analyses. In a preferred embodiment, the proteinsidentified using mass spectrometry are quantified and identified asenriched in the sample containing the tagged target chromatin comparedto the sample containing the untagged target chromatin using label-freeproteomics. In an exemplary embodiment, the proteins identified usingmass spectrometry are quantified and identified as enriched in thesample containing the tagged target chromatin compared to the samplecontaining the untagged target chromatin using spectral counting.

The method of protein quantification by spectral count is known in theart and is reviewed in Zhu et al., J Biomed Biotechnol 2010, which isincorporated by reference herein. In spectral counting, relative proteinquantification is achieved by comparing the number of identified MS/MSspectra from a protein of one sample to the same protein in the othersample. In the present invention, one sample comprises a targetchromatin that is tagged and another sample comprises a target chromatinthat is untagged. Protein quantification in spectral counting utilizesthe fact that an increase in protein abundance typically results in anincrease in the number of its proteolytic peptides, and vice versa. Thisincreased number of (tryptic) digests then usually results in anincrease in protein sequence coverage, the number of identified uniquepeptides, and the number of identified total MS/MS spectra (spectralcount) for each protein.

As such, determining the abundance of an identified protein in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, may determine if the protein was specifically associated with atarget chromatin of the invention. If an identified protein associatedwith a target chromatin is in enriched in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, then theprotein was specifically associated with a target chromatin of theinvention. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, then theprotein is non-specifically associated with a target chromatin of theinvention.

A skilled artisan in spectral counting will appreciate thatnormalization and statistical analysis of spectral counting datasets arenecessary for accurate and reliable detection of protein changes. Sincelarge proteins tend to contribute more peptide/spectra than small ones,a normalized spectral abundance factor (NSAF) is defined to account forthe effect of protein length on spectral count. NSAF is calculated asthe number of spectral counts (SpC) identifying a protein, divided bythe protein's length (L), divided by the sum of SpC/L for all proteinsin the experiment. NSAF allows the comparison of abundance of individualproteins in multiple independent samples and has been applied toquantify the expression changes in various complexes.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values. In an exemplary embodiment, proteins enriched ina sample containing a tagged target chromatin compared to a samplecontaining an untagged target chromatin are enriched by at least about 2fold. In other embodiments, proteins enriched in a sample containing atagged target chromatin compared to a sample containing the untaggedtarget chromatin are enriched by at least about 1.5 fold. In otherembodiments, proteins enriched in a sample containing a tagged targetchromatin compared to a sample containing an untagged target chromatinare enriched by at least about 3 fold, about 4 fold, about 5 fold, about6 fold, about 7 fold, about 8 fold, about 9 fold, about 10 fold, about11 fold, about 12 fold, about 13 fold, about 14 fold, about 15 fold,about 16 fold, about 17 fold, about 18 fold, about 19 fold or about 20fold. As such, a protein enriched by at least about 2 fold in a taggedchromatin sample compared to an untagged chromatin sample, isspecifically associated with the chromatin. For instance, a baseline fornon-specifically associated proteins may be proteins enriched by lessthan about 1.5 fold in a tagged chromatin sample compared to an untaggedchromatin sample, wherein one or more proteins are not associated withchromatin. Non-limiting examples of proteins not associated with achromatin may include enzymes required for metabolism, receptors, andribosomal proteins. In preferred embodiments, proteins not associatedwith a chromatin are ribosomal proteins, and a baseline fornon-specifically associated proteins is an enrichment less than about1.5 fold in a tagged chromatin sampled compared to an untagged chromatinsample. In an exemplary embodiment, proteins or protein fragmentsenriched by at least 15 fold in a tagged chromatin sample compared to anuntagged chromatin sample are specifically associated with a targetchromatin.

In preferred embodiments, a target chromatin is tagged in one cellsample and a target chromatin is untagged in a second cell sample, andMS analysis is used to identify proteins or protein fragments isolatedduring affinity purification of each sample, and label-free proteomicsis used to determine if a protein or a protein fragment is specificallyor non-specifically associated with the target chromatin. Methods ofderiving MS data to identify proteins or protein fragments are known inthe art, and may include using known computational techniques to distillMS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. Insome embodiments, MS data is derived using Rosetta Elucidator. In otherembodiments, MS data is derived using MaxQuant. In preferredembodiments, MS data is derived using Mascot Distiller.

III. Method of CRISPR-ChAP-MS

In yet another aspect, the invention provides a method of isolating andidentifying proteins specifically associated with a target chromatinusing the Cas9 and guide RNA (gRNA) components of the CRISPR system asdescribed in Example 6 and FIG. 9. The CRISPR-ChAP-MS approach providesa new tool to study epigenetic regulation. Identification of proteinsand histone PTMs at 1 kb resolution does not depend on a prioriknowledge of a protein/PTM target, which distinguishes this method fromtraditional ChIP. This third-generation technology provides quantitativeidentification of specifically bound proteins and histone PTMs with anenhanced ability to isolate targeted chromatin only requiringsite-directed mutagenesis to alter the gRNA for genomic targeting.

The present disclosure provides a method of identifying proteinsincluding proteins comprising posttranslational modificationsspecifically associated with a target chromatin in a cell. The methodcomprises providing a first cell sample comprising nucleic acid bindingproteins and the target chromatin, wherein the target chromatin istagged by contacting the target chromatin with a tag capable ofspecifically recognizing and binding one or more portions of the targetchromatin and wherein the tag comprises an affinity handle, and a secondcell sample comprising nucleic acid binding proteins and the targetchromatin, wherein the target chromatin is not tagged by contacting thetarget chromatin with a non-functional tag that is not capable ofspecifically recognizing and binding one or more portions of the targetchromatin and wherein the non-functional tag comprises an affinityhandle. Affinity handle from each sample is isolated wherein affinityhandle isolated from the first cell sample consists of affinity handlebound to tagged target chromatin bound to specifically associatednucleic acid binding proteins and affinity handle bound tonon-specifically associated nucleic acid binding proteins and affinityhandle isolated from the second cell sample consists of affinity handlebound to non-specifically associated nucleic acid binding proteins,wherein isolating the affinity handle enriches for the tagged targetchromatin. Bound protein in each cell sample is identified. Then, theamount of each bound protein in each cell sample is determined, whereinbound proteins that are enriched in the first cell sample as compared tothe second cell sample are specifically associated with the taggedchromatin in the first cell sample.

The key to success with the CRISPR-ChAP-MS is the enhanced ability toisolate targeted chromatin. Further, CRISPR-ChAP-MS only requiressite-directed mutagenesis to alter the gRNA for genomic targeting, whichprovides a more cost effective approach that can easily be multiplexedto target additional sites. The chromatin enrichment methodologydescribed herein is quantitative mass spectrometry used to determineproteins/PTMs specific to the isolated chromatin. The mass spectrometricapproach used in the CRISPR-ChAP-MS approach is label-free. Withlabel-free quantitative methods, each sample is separately prepared,then subjected to individual LC-MS/MS or LC/LC-MS/MS runs. The method ofspectral counting is used to categorize whether proteins enriched with asection of chromatin are specific or contaminant. As such, determiningthe abundance of an identified protein in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, maydetermine if the protein was specifically associated with the targetchromatin of the invention. If a protein associated with a targetchromatin is enriched in a tagged chromatin sample compared to the sameprotein in an untagged chromatin sample, then the protein isspecifically associated with the target chromatin. If an identifiedprotein is not enriched in a tagged chromatin sample compared to anuntagged chromatin sample, then association of that protein with thetarget chromatin is not specific.

(a) Cells

A target nucleic acid sequence may be isolated from any cell comprisingthe target nucleic acid sequence of the invention. According to theinvention, a method comprises, in part, providing a first cell sampleand a second cell sample. A cell of a cell sample of the invention maybe an archaebacterium, a eubacterium, or a eukaryotic cell. Forinstance, a cell of a cell sample of the invention may be a methanogen,a halophile or a thermoacidophile archaeabacterium, a gram positive, agram negative, a cyanobacterium, a spirochaete, or a firmicutebacterium, a fungal cell, a moss cell, a plant cell, an animal cell, ora protist cell.

In some embodiments, a cell of a cell sample of the invention is a cellfrom an animal. A cell from an animal cell may be a cell from an embryo,a juvenile, or an adult. Suitable animals include vertebrates such asmammals, birds, reptiles, amphibians, and fish. Examples of suitablemammals include without limit rodents, companion animals, livestock, andprimates. Non-limiting examples of rodents include mice, rats, hamsters,gerbils, and guinea pigs. Suitable companion animals include but are notlimited to cats, dogs, rabbits, hedgehogs, and ferrets. Non-limitingexamples of livestock include horses, goats, sheep, swine, cattle,llamas, and alpacas. Suitable primates include but are not limited tohumans, capuchin monkeys, chimpanzees, lemurs, macaques, marmosets,tamarins, spider monkeys, squirrel monkeys, and vervet monkeys.Non-limiting examples of birds include chickens, turkeys, ducks, andgeese. In some embodiments, a cell is a cell from a human.

In some embodiments, a cell of a cell sample may be from a modelorganism commonly used in laboratory research. For instance, a cell ofthe invention may be an E. coli, a Bacillus subtilis, a Caulobactercrescentus, a Mycoplasma genitalium, an Aliivibrio fischeri, aSynechocystis, or a Pseudomonas fluorescens bacterial cell; aChlamydomonas reinhardtii, a Dictyostelium discoideum, a Tetrahymenathermophila, an Emiliania huxleyi, or a Thalassiosira pseudonana protistcell; an Ashbya gossypii, an Aspergillus nidulans, a Coprinus cinereus,a Cunninghamella elegans, a Neurospora crassa, a Saccharomycescerevisiae, a Schizophyllum commune, a Schizosaccharomyces pombe, or anUstilago maydis fungal cell; an Arabidopsis thaliana, a Selaginellamoellendorffii, a Brachypodium distachyon, a Lotus japonicus, a Lemnagibba, a Zea mays, a Medicago truncatula, a Mimulus, a tobacco, a rice,a Populus, or a Nicotiana benthamiana plant cell; a Physcomitrellapatens moss; an Amphimedon queenslandica sponge, an Arbacia punctulatasea urchin, an Aplysia sea slug, a Branchiostoma floridae deuterostome,a Caenorhabditis elegans nematode, a Ciona intestinalis sea squirt, aDaphnia spp. crustacean, a Drosophila fruit fly, a Euprymna scolopessquid, a Hydra Cnidarian, a Loligo pealei squid, a Macrostomum lignanoflatworm, a Mnemiopsis leidyicomb jelly, a Nematostella vectensis seaanemone, an Oikopleura dioica free-swimming tunicate, an Oscarellacarmela sponge, a Parhyale hawaiensis crustacean, a Platynereisdumerilii marine polychaetous annelid, a Pristionchus pacificusroundworm, a Schmidtea mediterranea freshwater planarian, aStomatogastric ganglion of various arthropod species, aStrongylocentrotus purpuratus sea urchin, a Symsagittifera roscoffensisflatworm, a Tribolium castaneum beetle, a Trichoplax adhaerens Placozoa,a Tubifex tubifex oligochaeta, a laboratory mouse, a guinea pig, achicken, a cat, a dog, a hamster, a lamprey, a medaka fish, a rat, arhesus macaque, a cotton rat, a zebra finch, a Takifugu pufferfish, anAfrican clawed frog, or a zebrafish. In exemplary embodiments, a cell isa Saccharomyces cerevisiae yeast cell. In particularly exemplaryembodiments, a cell is a Saccharomyces cerevisiae W303a yeast cell.

A cell of a cell sample of the invention may be derived from a tissue orfrom a cell line grown in tissue culture. A cell line may be adherent ornon-adherent, or a cell line may be grown under conditions thatencourage adherent, non-adherent or organotypic growth using standardtechniques known to individuals skilled in the art. Cell lines andmethods of culturing cell lines are known in the art. Non-limitingexamples of cell lines commonly cultured in a laboratory may includeHeLa, a cell line from the National Cancer Institute's 60 cancer celllines, DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breastcancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breastcancer), THP-1 (acute myeloid leukemia), U87 (glioblastoma), SHSY5YHuman neuroblastoma cells, Saos-2 cells (bone cancer), Vero, GH3(pituitary tumor), PC12 (pheochromocytoma), MC3T3 (embryonic calvarium),Tobacco BY-2 cells, Zebrafish ZF4 and AB9 cells, Madin-Darby caninekidney (MDCK), or Xenopus A6 kidney epithelial cells.

A cell of a cell sample may be derived from a biological sample. As usedherein, the term “biological sample” refers to a sample obtained from asubject. Any biological sample containing a cell is suitable. Numeroustypes of biological samples are known in the art. Suitable biologicalsample may include, but are not limited to, tissue samples or bodilyfluids. In some embodiments, the biological sample is a tissue samplesuch as a tissue biopsy. The tissue biopsy may be a biopsy of a known orsuspected tumor. The biopsied tissue may be fixed, embedded in paraffinor plastic, and sectioned, or the biopsied tissue may be frozen andcryosectioned. Alternatively, the biopsied tissue may be processed intoindividual cells or an explant, or processed into a homogenate, a cellextract, a membranous fraction, or a protein extract. The sample mayalso be primary and/or transformed cell cultures derived from tissuefrom the subject. In other embodiments, the sample may be a bodilyfluid. Non-limiting examples of suitable bodily fluids include blood,plasma, serum, and urine. The fluid may be used “as is”, the cellularcomponents may be isolated from the fluid, or a protein fraction may beisolated from the fluid using standard techniques.

Suitable subjects include, but are not limited to, a human, a livestockanimal, a companion animal, a lab animal, and a zoological animal. Inone embodiment, the subject may be a rodent, e.g. a mouse, a rat, aguinea pig, etc. In another embodiment, the subject may be a livestockanimal. Non-limiting examples of suitable livestock animals may includepigs, cows, horses, goats, sheep, llamas and alpacas. In yet anotherembodiment, the subject may be a companion animal. Non-limiting examplesof companion animals may include pets such as dogs, cats, rabbits, andbirds. In yet another embodiment, the subject may be a zoologicalanimal. As used herein, a “zoological animal” refers to an animal thatmay be found in a zoo. Such animals may include non-human primates,large cats, wolves, and bears. In preferred embodiments, the animal is alaboratory animal. Non-limiting examples of a laboratory animal mayinclude rodents, canines, felines, and non-human primates. In apreferred embodiment, the subject is human.

As will be appreciated by a skilled artisan, the method of collecting abiological sample can and will vary depending upon the nature of thebiological sample and the type of analysis to be performed. Any of avariety of methods generally known in the art may be utilized to collecta biological sample. Generally speaking, the method preferably maintainsthe integrity of the sample such that chromatin can be accuratelydetected and measured according to the invention.

As described in Section III above, two cell samples, or lysates derivedfrom two cell samples may be subjected to mass-spectrometry coupled withlabel-free proteomics, one sample of which contains a tagged targetchromatin of the invention. Typically, cells in a first cell sample anda second cell sample of the invention are from the same type of cells ormay be derived from the same type of cells or derived from the samebiological sample. In some embodiments, cells may comprise aheterologous nucleic acid expressed in a cell of the invention, and mayalso comprise a heterologous protein expressed in a cell of theinvention. The heterologous nucleic acid and protein expressed in a cellmay be used for tagging a chromatin of the invention as described inSection III(c). In an exemplary embodiment, cells from a first cellsample may comprise a heterologous nucleic acid and protein expressed ina cell of the invention, and cells from a second cell sample maycomprise a heterologous protein expressed in a cell of the invention.

A first cell sample and a second cell sample of the invention may befrom the same genus, species, variety or strain of cells or from thesame biological sample. In an exemplary embodiment, a first cell sampleand a second cell sample of the invention are Saccharomyces cerevisiaeyeast cells.

The number of cells in a cell sample can and will vary depending on thetype of cells, the abundance of a target chromatin in a cell, and themethod of protein identification used, among other variables. Forinstance, about 1×10⁵ to about 1×10¹² cells may be used. Accordingly,about 1×10⁵, about 1×10⁶, about 1×10⁷, about 1×10⁸, about 1×10⁹, about1×10¹⁰, about 1×10¹¹, about 1×10¹², or more cells may be used.Preferably, about 1×10⁹ to about 1×10¹¹ cells may be used in a cellsample. In some embodiments, about 1×10¹⁰ cells are used in a cellsample. In an exemplary embodiment, about 1×10¹⁰ Saccharomycescerevisiae cells are used.

A first cell sample and a second cell sample of the invention aretypically grown identically. Identically grown cell samples minimizespotential structural or functional differences at a target chromatinpresent in both cell samples. As used herein, “grown identically” refersto cultured cell samples grown using similar culture condition, or cellsfrom a tissue harvested using identical harvesting techniques, orbiological samples collected, and optionally processed, via identicaltechniques.

(b) Chromatin

According to the invention, a first cell sample and a second cell sampleof the invention comprise nucleic acid binding proteins and a targetchromatin. As used herein, “nucleic acid binding proteins” refers toproteins that bind nucleic acid. Nucleic acid binding proteins areproteins that are composed of nucleic acid-binding domains and thus havespecific or general specificity for either single or double strandednucleic acid. A nucleic acid binding protein may bind nucleic acidspecifically or nonspecifically. Non-specific association of nucleicacid binding proteins with chromatin makes it challenging to identifyproteins that are specifically bound to chromatin. The methodology ofthe present disclosure overcomes this challenge by reducing the amountof non-specific proteins bound to chromatin and enriching for proteinsspecifically bound to chromatin.

As used herein, “chromatin” refers to a target nucleic acid sequencethat may be isolated from a cell. Generally, chromatin refers to thecombination of nucleic acids and proteins in the nucleus of a eukaryoticcell. However, it is contemplated that the term “chromatin” may alsorefer to the combination of a nucleic acid sequence and proteinsassociated with the nucleic acid sequence in a cell.

A chromatin of the invention may comprise single stranded nucleic acid,double stranded nucleic acid, or a combination thereof. In someembodiments, a chromatin comprises single stranded nucleic acid. Inother embodiments, a chromatin comprises a combination of singlestranded and double stranded nucleic acids. In yet other embodiments, achromatin comprises double stranded nucleic acid.

A chromatin of the invention may comprise a ribonucleic acid (RNA), adeoxyribonucleic acid (DNA), or a combination of RNA and DNA. In someembodiments, a chromatin of the invention comprises a combination of aRNA sequence and proteins associated with the RNA sequence in a cell.Non-limiting examples of RNA sequences may include mRNA, and non-codingRNA such as tRNA, rRNA, snoRNAs, microRNAs, siRNAs, piRNAs and the longnoncoding RNA (IncRNA). In preferred embodiments, a chromatin of theinvention comprises a combination of a DNA sequence and proteinsassociated with the DNA sequence in a cell. In other preferredembodiments, a chromatin of the invention comprises a combination of RNAand DNA sequences, and proteins associated with the RNA and DNA sequencein a cell. Non limiting examples of chromatin that may comprise acombination of RNA and DNA may include genomic DNA undergoingtranscription, or genomic DNA comprising non-coding RNA such as IncRNA.

A chromatin of the invention may be genomic chromatin such as, chromatinfrom a chromosome of a cell, or chromatin from an organelle in the cell.Alternatively, a chromatin may be chromatin from an extrachromosomalnucleic acid sequence. In some embodiments, a chromatin of the inventionis chromatin from an organelle in the cell. Non-limiting examples of achromatin from an organelle may include mitochondrial nucleic acidsequence in plant and animal cells, and a chloroplast nucleic acidsequence in plant cells. In some embodiments, a nucleic acid sequence ofthe invention is a mitochondrial nucleic acid sequence. In otherembodiments, a nucleic acid sequence of the invention is a chloroplastnucleic acid sequence.

In some embodiments, a chromatin of the invention is chromatin from anextrachromosomal nucleic acid sequence. The term “extrachromosomal,” asused herein, refers to any nucleic acid sequence not contained withinthe cell's genomic nucleic acid sequence. An extrachromosomal nucleicacid sequence may comprise some sequences that are identical or similarto genomic sequences in the cell, however, an extrachromosomal nucleicacid sequence as used herein does not integrate with genomic sequencesof the cell. Non-limiting examples of an extrachromosomal nucleic acidsequence may include a plasmid, a virus, a cosmid, a phasmid, and aplasmid.

In some preferred embodiments, a chromatin of the invention is genomicchromatin. In exemplary embodiments, a chromatin of the invention isgenomic chromatin of a eukaryotic cell. A eukaryotic cell of theinvention may be as described in Section III(a) above.

Primary functions of genomic chromatin of a eukaryotic cell may be DNApackaging into a smaller volume to fit in the cell, strengthening of theDNA to allow mitosis, prevent DNA damage, and to control gene expressionand DNA replication. As described above, genomic chromatin of aeukaryotic cell may comprise DNA sequences and a plurality ofDNA-binding proteins as well as certain RNA sequences, assembled intohigher order structural or functional regions. As used herein, a“structural or functional feature of a chromatin”, refers to a chromatinfeature characterized by, or encoding, a function such as a regulatoryfunction of a promoter, terminator, translation initiation, enhancer,etc., or a structural feature such as heterochromatin, euchromatin, anucleosome, a telomere, or a centromere. A physical feature of a nucleicacid sequence may comprise a functional role and vice versa. Asdescribed below, a chromatin of the invention may be a chromatinfragment, and as such may comprise a fragment of a physical orfunctional feature of a chromatin, or no physical or functional featuresor known physical or functional features.

The primary protein components of genomic eukaryotic chromatin arehistones that compact the DNA into a nucleosome. The nucleosomecomprises an octet of histone proteins around which is wound a stretchof double stranded DNA sequence of about 150 to about 250 bp in length.Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1may act to link adjacent nucleosomes together into a higher orderstructure. Histones are subject to post translational modification whichmay affect their function in regulating chromatin function. Suchmodifications may include methylation, citrullination, acetylation,phosphorylation, SUMOylation, ubiquitination, and ADP-ribosylation.

Many further polypeptides and protein complexes interact with thenucleosome and the histones to regulate chromatin function. A“polypeptide complex” as used herein, is intended to describe proteinsand polypeptides that assemble together to form a unitary association offactors. The members of a polypeptide complex may interact with eachother via non-covalent or covalent bonds. Typically members of apolypeptide complex will cooperate to enable binding either to a nucleicacid sequence or to polypeptides and proteins already associated with orbound to a nucleic acid sequence in chromatin. Chromatin associatedpolypeptide complexes may comprise a plurality of proteins and/orpolypeptides which each serve to interact with other polypeptides thatmay be permanently associated with the complex or which may associatetransiently, dependent upon cellular conditions and position within thecell cycle. Hence, particular polypeptide complexes may vary in theirconstituent members at different stages of development, in response tovarying physiological conditions or as a factor of the cell cycle. Byway of example, in animals, polypeptide complexes with known chromatinremodelling activities include Polycomb group gene silencing complexesas well as Trithorax group gene activating complexes.

A chromatin of the invention may be an intact and complete chromatinfrom the cell, or may be a fragment of a chromatin in a cell. In someembodiments, a chromatin of the invention is an intact chromatinisolated from a cell. For instance, a chromatin of the invention may bea plasmid, a cosmid, or a phage chromatin or a complete organellarchromatin. In preferred embodiments, a chromatin of the invention is afragment of a chromatin from a cell. In exemplary embodiments, achromatin of the invention is a fragment of a genomic chromatin from acell.

When a chromatin of the invention is a fragment of a chromatin in acell, any method of fragmenting a chromatin known in the art may beused. Such methods may include physical methods of fragmenting achromatin, or enzymatic digestion of a nucleic acid sequence of achromatin. In some embodiments, a fragment of a chromatin may begenerated using enzymatic digestion of a nucleic acid sequence inchromatin. Non-limiting examples of enzymatic digestion may includerandom or sequence specific enzymatic digestion using restrictionenzymes, nucleases, combinations of restriction enzymes and nucleases,or combinations of nicking and other nucleases such as NEBNext™fragmentase, which comprises a nicking enzyme that randomly generatesnicks in double stranded DNA and another enzyme that cuts the strandopposite to the generated nicks.

In other embodiments, a fragment of a chromatin may be generated using aphysical method of fragmenting a chromatin. Non-limiting examples ofphysical fragmenting methods that may be used to fragment a chromatin ofthe invention may include nebulization, sonication, and hydrodynamicshearing. In some embodiments, a fragment of a chromatin may begenerated using nebulization. In other embodiments, a fragment of achromatin may be generated using hydrodynamic shearing. In preferredembodiments, a fragment of a chromatin may be generated usingsonication. During sonication, a sample comprising chromatin issubjected to ultrasonic waves, whose vibrations produce gaseouscavitations in the liquid that shear or break high molecular weightmolecules such as chromatin through resonance vibration. Sonicationmethods that may be used to generate a chromatin of the invention areknown in the art

A fragment of a chromatin of the invention may comprise a nucleic acidsequence fragment and may be about 10, 50, 100, 150, 200, 250, 300, 350,400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050,1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650,1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, 2250,2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850,2900, 2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000bases long or more. In some embodiments, a chromatin of the inventionmay comprise a nucleic acid sequence fragment of about 10, 20, 30, 40,50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470,480, 490, or about 500 bases long. In other embodiments, a chromatin ofthe invention may comprise a nucleic acid sequence fragment of about500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630,640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, or about 1000 bases long. In yetother embodiments, a chromatin of the invention may comprise a nucleicacid sequence fragment of about 1000, 1010, 1020, 1030, 1040, 1050,1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160, 1170,1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280, 1290,1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400, 1410,1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500 baseslong. In other embodiments, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1500, 1510, 1520, 1530, 1540,1550, 1560, 1570, 1580, 1590, 1600, 1610, 1620, 1630, 1640, 1650, 1660,1670, 1680, 1690, 1700, 1710, 1720, 1730, 1740, 1750, 1760, 1770, 1780,1790, 1800, 1810, 1820, 1830, 1840, 1850, 1860, 1870, 1880, 1890, 1900,1910, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, or about 2000bases long. In additional embodiments, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 2000, 2100, 2150,2200, 2250, 2300, 2350, 2400, 2450, or about 2500 bases long. In otherembodiments, a chromatin of the invention may comprise a nucleic acidsequence fragment of about 2000, 2050, 2100, 2150, 2200, 2250, 2300,2350, 2400, 2450, or about 2500 bases long. In still other embodiments,a chromatin of the invention may comprise a nucleic acid sequencefragment of about 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900,2950, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or about 10000 baseslong or more.

In some preferred embodiments, a chromatin fragment of the invention maycomprise a nucleic acid sequence fragment of about 550, 560, 570, 580,590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720,730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860,870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120,1130, 1140, 1150, 1160, 1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240,or about 1250 bases long. In a preferred embodiment, a chromatin of theinvention may comprise a nucleic acid sequence fragment of about 750,760, 770, 780, 790, 800, 810, 820, 830, 840, or about 850 bases long. Inanother preferred embodiment, a chromatin of the invention may comprisea nucleic acid sequence fragment of about 950, 960, 970, 980, 990, 1000,1010, 1020, 1030, 1040, or about 1050 bases long.

In other preferred embodiments, a chromatin fragment of the inventionmay comprise a nucleic acid sequence fragment of about 750, 760, 770,780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910,920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040,1050, 1060, 1070, 1080, 1090, 1100, 1110, 1120, 1130, 1140, 1150, 1160,1170, 1180, 1190, 1200, 1210, 1220, 1230, 1240, 1250, 1260, 1270, 1280,1290, 1300, 1310, 1320, 1330, 1340, 1350, 1360, 1370, 1380, 1390, 1400,1410, 1420, 1430, 1440, 1450, 1460, 1470, 1480, 1490, or about 1500bases long. In a preferred embodiment, a chromatin of the invention maycomprise a nucleic acid sequence fragment of about 950, 960, 970, 980,990, 1000, 1010, 1020, 1030, 1040, or about 1050 bases long. In anotherpreferred embodiment, a chromatin of the invention may comprise anucleic acid sequence fragment of about 1200, 1210, 1220, 1230, 1240,1250, 1260, 1270, 1280, 1290, or about 1300 bases long.

As described in this section above, a chromatin of the invention maycomprise one or more nucleosomes. As such, a chromatin fragment of theinvention may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, or about 20 nucleosomes. In some embodiments, achromatin fragment of the invention may comprise about 1, 2, 3, 4, orabout 5 nucleosomes. In other embodiments, a chromatin fragment of theinvention may comprise about 5, 6, 7, 8, 9, or about 10 nucleosomes. Inyet other embodiments, a chromatin fragment of the invention maycomprise about 10, 11, 12, 13, 14, or about 15 nucleosomes. In otherembodiments, a chromatin fragment of the invention may comprise about15, 16, 17, 18, 19, or about 20 nucleosomes. In preferred embodiments, achromatin fragment of the invention may comprise about 4 nucleosomes. Inother preferred embodiments, a chromatin fragment of the invention maycomprise about 5 nucleosomes.

A target chromatin fragment of the invention may comprise a structuralor a functional feature of chromatin as described above, a fragment of aphysical or functional feature, or no physical or functional features orknown physical or functional features. In some embodiments, a targetchromatin fragment of the invention comprises a structural feature ofchromatin. In other embodiments, a target chromatin fragment of theinvention comprises no physical or functional features or known physicalor functional features. In yet other embodiments, a target chromatinfragment of the invention comprises a functional feature of chromatin.In exemplary embodiments, a target chromatin is a promoter.

(c) Tagging the Target Chromatin

According to the invention, a target chromatin from a first cell sampleis tagged and a target chromatin from a second cell sample is nottagged. In essence, tagging a target chromatin may comprise contactingthe target chromatin of the invention with a tag capable of specificallyrecognizing and binding one or more portions of a target chromatin. Asused herein, “specifically recognizing” refers to a binding reactionbetween two separate molecules that is at least two times the backgroundand more typically more than 10 to 100 times the background molecularassociations under physiological conditions. A tag may be capable ofspecifically recognizing and binding 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10components of a target chromatin. In preferred embodiments, a tag iscapable of specifically recognizing and binding one component of atarget chromatin. Alternatively, not tagging a target chromatin maycomprise contacting the target chromatin with a non-functional tag thatis not capable of specifically recognizing and binding one or moreportions of the target chromatin. Specifically, the non-functional taglacks a component of the tag that is essential for specificallyrecognizing and thus tagging the target chromatin.

A tag may be capable of specifically recognizing and binding a componentin a target chromatin. A component in a target chromatin may be anucleic acid sequence in a nucleic acid associated with a targetchromatin, a protein associated with a target chromatin, or a chromatinstructural or functional feature in a target chromatin. A nucleic acidsequence associated with a target chromatin that may be specificallyrecognized and bound by a tag of the invention may be a nucleic acidsequence normally found in a chromatin of a cell of the invention.

Individuals of ordinary skill in the art will recognize that anexogenous component introduced into a cell to facilitate tagging atarget chromatin of the invention cannot and will not disrupt a targetchromatin, or a structural or functional feature of a target chromatin.Methods of designing a chromatin component and a tag capable of bindingthe chromatin component that does not disrupt a chromatin of theinvention may depend on the particular application of a method of theinvention, and may be determined experimentally. For instance, if anapplication of a method of the invention comprises promoter function, atag may be designed to bind anywhere adjacent to the promoter, butwithout disrupting the promoter.

In an embodiment, a tag of the invention comprises a nucleic acidsequence capable of binding a nucleic acid sequence component of atarget chromatin, wherein the nucleic acid sequence component of thechromatin is normally present in a cell of the invention. Non-limitingexamples of nucleic acids capable of binding a nucleic acid sequencecomponent of a chromatin include antisense RNA or DNA nucleic acids, andmodified nucleic acids and nucleic acid mimics such as peptide nucleicacids, locked nucleic acids, phosphorodiamidate morpholino oligomers(PMO). In some embodiments, a tag of the invention comprises a nucleicacid sequence comprising locked nucleotides. For instance, a nucleicacid sequence comprising locked nucleotides may be as described inUS20110262908 or US20120040857, and a peptide nucleic acid tag may be asdescribed in Boffa et al. 1995 PNAS 92:1901-1905, the disclosures of allof which are incorporated herein in their entirety. Importantly, anon-functional tag of the invention lacks the nucleic acid component ofthe tag such that the non-functional tag is not capable of specificallyrecognizing a nucleic acid sequence component of a target chromatin.

In specific embodiments, a tag of the invention comprises a guide RNA(gRNA) capable of binding a nucleic acid sequence component of achromatin, wherein the nucleic acid sequence component of the chromatinis normally present in a cell of the invention. A gRNA may be part ofthe Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)Type II system. There are two distinct components to this system: (1) aguide RNA and (2) an endonuclease, in this case the CRISPR associated(Cas) nuclease, Cas9. The guide RNA is a combination of the endogenousbacterial crRNA and tracrRNA into a single chimeric guide RNA (gRNA)transcript. The gRNA combines the targeting specificity of the crRNAwith the scaffolding properties of the tracrRNA into a singletranscript. When the gRNA and the Cas9 are expressed in the cell, thegRNA/Cas9 complex is recruited to the target sequence by thebase-pairing between the gRNA sequence and the complement to the targetsequence in the genomic DNA. For successful binding of Cas9, the genomictarget sequence must also contain the correct Protospacer AdjacentMotiff (PAM) sequence immediately following the target sequence. Thebinding of the gRNA/Cas9 complex localizes the Cas9 to the genomictarget sequence. Accordingly, guide RNA corresponds to a nucleic acidcomprising a complementary sequence to a nucleic acid sequence componentof a chromatin. In the present invention, guide RNA is engineered tocomprise a sequence complementary to a portion of a nucleic acidsequence component of a chromatin such that it is capable of targetingthe nucleic acid sequence component of a chromatin. In a particularembodiment, the guide RNA comprises a sequence of 5 to 50 nucleotides,preferably at least 12 nucleotides which is complementary to the nucleicacid sequence component of a chromatin. In a more particular embodiment,the guide RNA is a sequence of at least 30 nucleotides which comprisesat least 10 nucleotides, preferably 12 nucleotides complementary to thenucleic acid sequence component of a chromatin. In certain embodiments,a target nucleic add sequence comprises a PAM sequence immediatelyfollowing the nucleic acid sequence component of a chromatin. Thetypical length of the nucleic acid sequence component of a chromatin isabout 20 base pairs, although sequences that are longer or shorter canbe used.

A tag of the invention further comprises a protein that associates withthe nucleic acid portion of the tag. Accordingly, a tag furthercomprises a protein capable of binding the nucleic acid portion of thetag, wherein the nucleic acid portion of the tag specifically recognizesa nucleic acid sequence normally found in a cell of the invention. Theprotein may be a wild type nucleic acid binding protein capable ofbinding a nucleic acid tag bound to a target chromatin. Alternatively,the protein may be engineered to have binding specificity for thenucleic acid portion of the tag. In preferred embodiments, the proteincomprises a nuclease inactivated Cas9 protein, or derivatives thereof,wherein the Cas9 protein binds to the nucleic acid portion of the tag ofthe invention. In exemplary embodiments, a tag comprises Cas9, whereinCas9 binds to guide RNA (gRNA). Importantly, the non-functional tagcomprises the same protein as the functional tag of the invention.

A tag of the invention further comprises an affinity handle. An affinityhandle may be used as an affinity purification handle for purifying atagged target chromatin. Affinity handles may include any affinityhandle for which a cognate binding agent is readily available. Anaffinity handle may be an aptamer, an antibody, an antibody fragment, adouble-stranded DNA sequence, modified nucleic acids and nucleic acidmimics such as peptide nucleic acids, locked nucleic acids,phosphorodiamidate morpholino oligomers (PMO), a ligand, a ligandfragment, a receptor, a receptor fragment, a polypeptide, a peptide, acoenzyme, a coregulator, an allosteric molecule, non-immunoglobulinscaffolds such as Affibodies, Anticalins, designed Ankyrin repeatproteins and others, an ion, or a small molecule for which a cognatebinding agent is readily available. The term “aptamer” refers to apolypeptide or a polynucleotide capable of binding to a target moleculeat a specific region. It is generally accepted that an aptamer, which isspecific in its binding to any polypeptide, may be synthesized and/oridentified by in vitro evolution methods. Non limiting examples ofhandles that may be suitable for isolating a chromatin may includebiotin or a biotin analogue such as desthiobiotin, digoxigenin,dinitrophenol or fluorescein, a macromolecule that binds to a nucleicacid or a nucleic acid binding protein such as the Lac repressor, a zincfinger protein, a transcription activator protein capable of binding anucleic acid, or a transcription activator-like (TAL) protein, antigenicpolypeptides such as protein A, or peptide ‘tags’ such as polyhistidine,FLAG, HA and Myc tags. In preferred embodiments, an affinity handle maybe an antigenic polypeptide. In specific embodiments, an affinity handlemay be the protein A antigenic polypeptide, or derivatives thereof. Dueto the properties of an affinity handle, the affinity handle may alsonon-specifically associate with nucleic acid binding proteins.Importantly, the non-functional tag comprises the same affinity handleas the functional tag of the invention.

In specific embodiments, a tag of the invention comprises protein A asthe affinity handle. In other specific embodiments, a tag of theinvention comprises catalytically inactive Cas9 nuclease as the protein.In exemplary embodiments, a tag of the invention comprises protein A anda catalytically inactive Cas9 nuclease. In another exemplary embodiment,a tag of the invention comprises protein A tagged nuclease inactivatedCas9 protein and a gRNA which has been modified to bind a nucleic acidsequence normally found in a cell. In still another exemplaryembodiment, a non-functional tag of the invention comprises protein Atagged nuclease inactivated Cas9 protein and does not comprise a gRNA.The Cas9 and gRNA of the invention may be components of the CRISPRsystem as discussed above.

A target chromatin may be contacted with a tag or non-functional tag atany time during a method of the invention leading to isolation of targetchromatin. For instance, a target chromatin may be contacted with a tagor non-functional tag during cell culture by expressing the tag ornon-functional tag in a cell of the invention. Alternatively, a targetchromatin may be contacted with a tag or non-functional tag after cellculture but before cell lysis, after cell lysis, or after fragmentationof chromatin to generate chromatin fragments comprising a targetchromatin. In such embodiments, a tag or non-functional tag may be addedto the cell culture or cell lysate as a recombinant protein. Therecombinant protein may be expressed, isolated and purified via methodsstandard in the art for protein purification.

In some embodiments, a target chromatin is contacted with a tag ornon-functional tag after cell culture but before cell lysis. As such, atag or non-functional tag may be introduced into a cell before celllysis. Methods of introducing a tag or non-functional tag into a cell ofthe invention can and will vary depending on the type of cell, the tag,and the application of a method of the invention. For instance, anucleic acid (i.e. a plasmid) capable of expressing a tag ornon-functional tag of the invention may be introduced into a cell afterculture such that the tag or non-functional tag is expressed during cellculture. In other embodiments, a target chromatin is contacted with atag or non-functional tag after cell lysis. In yet other embodiments, atarget chromatin is contacted with a tag or non-functional tag aftercell lysis and chromatin fragmentation. In both of the foregoingembodiments, the tag or non-functional tag may be introduced as arecombinant protein. In specific embodiments, a target chromatin iscontacted with a tag or non-functional tag during cell culture byexpressing the tag or non-functional tag in a cell of the inventionduring cell culture. In an exemplary embodiment, a target chromatin iscontacted with a tag during cell culture by expressing a tag comprisinga gRNA, inactivated Cas9, and an affinity handle in a cell of theinvention during cell culture. In another exemplary embodiment, a targetchromatin is contacted with a non-functional tag during cell culture byexpressing a tag comprising an inactivated Cas9 and an affinity handlein a cell of the invention during cell culture, wherein thenon-functional tag does not comprise a gRNA.

(d) Preparation of Cell Lysate

According to the invention, affinity handle bound to a tagged targetchromatin bound to nucleic acid binding proteins and affinity handlebound to non-specific nucleic acid binding proteins in a first cellsample is isolated and affinity handle bound to non-specific nucleicacid binding proteins in a second cell sample is isolated. The method ofisolating affinity handle in a first cell sample and second cell samplemay be performed on a cell lysate derived from a cell sample. A skilledpractitioner of the art will appreciate that structural and functionalfeatures of an affinity handle and a tagged target chromatin must bepreserved during cell lysis and isolation of the affinity handle and thetagged target chromatin. The association of proteins with a taggedtarget chromatin may be preserved during cell lysis using methods knownin the art for preserving a complex of proteins with a nucleic acidsequence. For instance, lysing of a cell may be performed underrefrigeration or using cryogenic methods and buffer conditions capableof preserving association of proteins and nucleic acid sequences. Inaddition, a complex of proteins with a nucleic acid may be preserved bycrosslinking protein and nucleic acid complexes in a cell prior tolysing. Crosslinking protein and nucleic acid complexes in a cell mayalso capture, or preserve, transient protein-protein and protein-nucleicacid interactions.

In some embodiments, a complex of proteins with a nucleic acid may bepreserved by crosslinking protein and nucleic acid complexes in achromatin prior to lysing a cell and isolating the affinity handle andtarget chromatin. Crosslinking is the process of joining two or moremolecules such as two proteins or a protein and a nucleic acid molecule,by a covalent bond. Molecules may be crosslinked by irradiation withultraviolet light, or by using chemical crosslinking reagents. Chemicalcrosslinking reagents capable of crosslinking proteins and nucleic acidsare known in the art and may include crosslinking reagents that targetamines, sulfhydryls, carboxyls, carbonyls or hydroxyls; omobifunctionalor heterobifunctional crosslinking reagent, variable spacer arm lengthor zero-length crosslinking reagents, cleavable or non-cleavablecrosslinking reagents, and photoreactive crosslinking reagents.Non-limiting examples of crosslinking reagents that may be used tocrosslink protein complexes and/or protein complexes and nucleic acidsmay include formaldehyde, glutaraldehyde, disuccinimidyl glutarate,disuccinimidyl suberate, a photoreactive amino acid such asphoto-leucine or photo-methionine, and succinimidyl-diazirine. Thedegree of crosslinking can and will vary depending on the application ofa method of the invention, and may be experimentally determined.

In a preferred embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehyde.In an exemplary embodiment, a complex of proteins with a nucleic acid ina chromatin of the invention may be preserved by crosslinking proteinand nucleic acid complexes in a cell prior to lysing using formaldehydeas described in the examples.

A skilled practitioner of the art will appreciate that protocols forlysing a cell can and will vary depending on the type of cell, thetarget chromatin of the invention, and the specific application of amethod of the invention. Non-limiting examples of methods that may beused to lyse a cell of the invention may include cell lysis using adetergent, an enzyme such as lysozyme, incubation in a hypotonic bufferwhich causes a cell to swell and burst, mechanical disruption such asliquid homogenization by forcing a cell through a narrow space,sonication, freeze/thaw, mortar and pestle, glass beads, andcombinations thereof. In some embodiments, when a cell of the inventionis a yeast cell, the cell may be cryogenically lysed under liquidnitrogen temperature with glass beads. In exemplary embodiments, when acell of the invention is a yeast cell, the cell may be cryogenicallylysed under liquid nitrogen temperature with glass beads as described inthe examples.

Buffer conditions used during lysing and isolation of a chromatin of theinvention can and will be altered to control stringent conditions duringcell lysis and isolation to preserve association of proteins and nucleicacid sequences of a chromatin. “Stringent conditions” in the context ofchromatin isolation are conditions capable of preserving specificassociation of proteins and nucleic acids of a chromatin, but minimizingnon-specific association of proteins and nucleic acids. Stringentcondition can and will vary depending on the application of a method ofthe invention, the target chromatin of the invention, the nucleic acidsequence in a target chromatin, the proteins or protein complexesassociated with a target chromatin of the invention, whether or notproteins, protein complexes and nucleic acid sequences are crosslinked,and the conditions used for crosslinking proteins, protein complexes andnucleic acid sequences of a target chromatin. For instance, morestringent buffer conditions may be used in a method of the inventionwherein proteins, protein-protein complexes, and protein-nucleic acidcomplexes are crosslinked compared to a method of the invention whereinproteins, protein-protein complexes, and protein-nucleic acid complexesare not crosslinked. As such, stringent buffer conditions used duringcell lysis and isolation of a nucleic acid sequence of the invention maybe experimentally determined for each application wherein a method ofthe invention is used. Buffer conditions that may alter stringentconditions during cell lysis and isolation may include pH and saltconcentration. In preferred embodiments, proteins, protein-proteincomplexes, and protein-nucleic acid complexes of a target chromatin ofthe invention are crosslinked, and stringent buffer conditions are usedduring lysis and isolation of a chromatin of the invention. In exemplaryembodiments, proteins, protein-protein complexes, and protein-nucleicacid complexes of a target chromatin of the invention are crosslinked,and stringent buffer conditions are used during lysis and isolation of achromatin of the invention and are as described in the examples. In anexemplary embodiment, a first cell sample and a second cell sample arecrosslinked to stabilize protein-protein and protein-nucleic acidinteractions with a target chromatin, then the first cell sample and thesecond cell sample are lysed, and then the target chromatin in the firstcell sample and the second cell sample is fragmented resulting in 500 to1500 base pair fragments.

(e) Chromatin Isolation

According to the invention, the method of isolating an affinity handlefrom each cell sample may be performed on cell lysates derived from thecell samples. As described in Sections III(d) above, a cell lysatecomprises a lysate of a cell sample, wherein a target chromatin istagged in one of the lysates, or one of the cell samples. A cell lysatealso comprises a lysate of a cell sample, wherein a target chromatin isnot tagged in one of the lysates, or one of the cell samples.

Isolating an affinity handle may enrich for a tagged target chromatin.An affinity handle bound to a tagged target chromatin may be isolatedfrom a mixture of chromatins or chromatin fragments in a cell lysate. Asused herein, the term “isolated” or “purified” may be used to describe apurified preparation of a target chromatin that is enriched for thetarget chromatin, but wherein the target chromatin is not necessarily ina pure form due to the presence of non-specifically bound nucleic acidbinding proteins. A target chromatin of the present invention may bepurified to homogeneity or other degrees of purity. In general, thelevel of purity of an isolated target chromatin can and will varydepending on the cell type, the specific chromatin to be isolated, andthe intended use of a target chromatin of the invention. The level ofpurity of an isolated target chromatin may be determined using methodsknown in the art. For instance, the level of purity of an isolatedtarget chromatin may be determined by determining the level of purity ofa nucleic acid sequence associated with a target chromatin, bydetermining the level of purity of a protein associated with a targetchromatin, or by determining the level of enrichment of a targetchromatin, compared to a non-target chromatin in a cell. In preferredembodiments, the level of purity of an isolated target chromatin isdetermined by determining the level of enrichment of a target chromatin,compared to a non-target chromatin in a cell.

For example, an isolated target chromatin is not necessarily 100% pure,but may be about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% pure. Anisolated target chromatin may be enriched for the target chromatin,relative to a chromatin in the lysed preparation that was contacted witha non-functional tag of the invention. An isolated target chromatin maybe enriched by 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold relative to achromatin that was contacted with a non-functional tag of the invention.In some embodiments, an isolated target chromatin is enriched by 10, 20,30, 40 or 50 fold relative to a chromatin that was contacted with anon-functional tag of the invention. In other embodiments, an isolatedtarget chromatin is enriched by 50, 60, 70, 80, 90, or 100 fold relativeto a chromatin that was was contacted with a non-functional tag of theinvention. In an exemplary embodiment, an isolated target chromatin isenriched 60, 65, 70, 75 or 80 fold relative to a chromatin that wascontacted with a non-functional tag of the invention.

An affinity handle may be isolated using methods known in the art, suchas electrophoresis, molecular, immunological and chromatographictechniques, ion exchange, hydrophobic, affinity, and reverse-phase HPLCchromatography, size exclusion chromatography, precipitation, dialysis,chromatofocusing, ultrafiltration and diafiltration techniques, andcombinations thereof. For general guidance in suitable purificationtechniques, see Scopes, R., Protein Purification, Springer-Vertag, NY(1982).

In general, a method of the invention comprises isolating an affinityhandle by affinity purification, or affinity purification in combinationwith other methods of isolating chromatin described above. In apreferred embodiment, a method of the invention comprises isolating anaffinity handle by affinity purification. Non limiting examples ofaffinity purification techniques that may be used to isolate an affinityhandle may include affinity chromatography, immunoaffinitychromatography, size exclusion chromatography, and combinations thereof.See, for example, Roe (ed), Protein Purification Techniques: A PracticalApproach, Oxford University Press, 2nd edition, 2001.

A target chromatin contacted and bound by a tag may be isolated usingany affinity purification method known in the art. In short, a targetchromatin is bound to an affinity handle capable of binding to asubstrate. The substrate comprising a bound affinity handle bound totarget chromatin may then be washed to remove non-target chromatin andother cell debris, and the target chromatin may be released fromsubstrate. Methods of affinity purification of material comprising anaffinity handle are known in the art and may include binding theaffinity handle to a substrate capable of binding the affinity handle.The substrate may be a gel matrix such as gel beads, the surface of acontainer, or a chip. The target chromatin bound to the affinity handlemay then be purified. Methods of purifying tagged molecules are known inthe art and will vary depending on the target molecule, the tag, and thesubstrate. For instance, if the affinity handle is bound to a targetchromatin, the affinity handle may be bound to a magnetic bead substratecomprising IgG, and purified using a magnet. Importantly, thenon-functional tag comprising an affinity handle in the second cellsample is subjected to the same affinity purification method as thefirst cell sample.

(f) Protein Extraction, Identification, and Determination of Labeling

Proteins and peptides associated with an isolated tagged targetchromatin are extracted from the isolated tagged target chromatin.Methods of extracting proteins from chromatin are generally known in theart of protein biochemistry. Generally, any extraction protocol suitablefor isolating proteins and known to those of skill in the art may beused. Extracted proteins may also be further purified before proteinidentification. For instance, protein extracts may be further purifiedby differential precipitation, differential solubilization,ultracentrifugation, using chromatographic methods such as sizeexclusion chromatography, hydrophobic interaction chromatography, ionexchange chromatography, affinity chromatography, metal binding,immunoaffinity chromatography, HPLC, or gel electrophoriesis such asSDS-PAGE and QPNC-PAGE. In a preferred embodiment, extracted proteinsare further purified using SDS-PAGE.

Extracted and purified intact proteins and post-translationalmodification of proteins may then be identified. Alternatively,extracted and purified intact proteins may be further digested, and theresulting peptide fragments are identified. In some embodiments, intactextracted proteins are identified. In preferred embodiments, extractedproteins are further digested, and the resulting peptide fragments areidentified. For instance, protein extracts may be fragmented byenzymatically digesting the proteins using a protease such as trypsin.In exemplary embodiments, extracted proteins are further digested asdescribed in the examples.

Methods of identifying proteins or protein fragments are known in theart and may include mass spectrometry (MS) analysis, or a combination ofmass spectrometry with a chromatographic technique. Non limitingexamples of mass spectrometer techniques may include tandem massspectrometry (MS/MS), matrix-assisted laser desorption/ionization sourcewith a time-of-flight mass analyzer (MALDI-TOF), inductively coupledplasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS),thermal ionization-mass spectrometry (TIMS), isotope ratio massspectrometry (IRMS), and spark source mass spectrometry (SSMS).Chromatographic techniques that may be used with MS may include gaschromatography, liquid chromatography, and ion mobility spectrometry. Ina preferred embodiment, proteins may be identified using tandem massspectrometry in combination with liquid chromatography (LC-MS/MS). Inanother preferred embodiment, post-translational modification ofproteins may be identified using tandem mass spectrometry in combinationwith liquid chromatography (LC-MS/MS).

In the present invention, the method of label-free proteomics is used tocategorize whether proteins enriched with a section of chromatin arespecific or contaminant. Label-free methods of quantifying proteins orprotein fragments are known in the art. In label-free quantitativeproteomics, each sample is separately prepared, then subjected toindividual methods of identifying proteins or protein fragments whichmay include LC-MS/MS or LC/LC-MS/MS. According to the invention, onesample comprises a target chromatin that is tagged in the cell sampleand one sample comprises a target chromatin that is untagged in the cellsample. Label-free protein quantification is generally based on twocategories of measurement. In the first are the measurements of ionintensity changes such as peptide peak areas or peak heights inchromatography. The second is based on the spectral counting ofidentified proteins after MS/MS analysis. Peptide peak intensity orspectral count is measured for individual LC-MS/MS or LC/LC-MS/MS runsand changes in protein abundance are calculated via a direct comparisonbetween different analyses. In a preferred embodiment, the proteinsidentified using mass spectrometry are quantified and identified asenriched in the sample containing the tagged target chromatin comparedto the sample containing the untagged target chromatin using label-freeproteomics. In an exemplary embodiment, the proteins identified usingmass spectrometry are quantified and identified as enriched in thesample containing the tagged target chromatin compared to the samplecontaining the untagged target chromatin using spectral counting.

The method of protein quantification by spectral count is known in theart and is reviewed in Zhu et al., J Biomed Biotechnol 2010, which isincorporated by reference herein. In spectral counting, relative proteinquantification is achieved by comparing the number of identified MS/MSspectra from a protein of one sample to the same protein in the othersample. In the present invention, one sample comprises a targetchromatin that is tagged and another sample comprises a target chromatinthat is untagged. Protein quantification in spectral counting utilizesthe fact that an increase in protein abundance typically results in anincrease in the number of its proteolytic peptides, and vice versa. Thisincreased number of (tryptic) digests then usually results in anincrease in protein sequence coverage, the number of identified uniquepeptides, and the number of identified total MS/MS spectra (spectralcount) for each protein.

As such, determining the abundance of an identified protein in a taggedchromatin sample compared to the same protein in an untagged chromatinsample, may determine if the protein was specifically associated with atarget chromatin of the invention. If an identified protein associatedwith a target chromatin is in enriched in a tagged chromatin samplecompared to the same protein in an untagged chromatin sample, then theprotein was specifically associated with a target chromatin of theinvention. If an identified protein is not enriched in a taggedchromatin sample compared to an untagged chromatin sample, then theprotein is non-specifically associated with a target chromatin of theinvention.

A skilled artisan in spectral counting will appreciate thatnormalization and statistical analysis of spectral counting datasets arenecessary for accurate and reliable detection of protein changes. Sincelarge proteins tend to contribute more peptide/spectra than small ones,a normalized spectral abundance factor (NSAF) is defined to account forthe effect of protein length on spectral count. NSAF is calculated asthe number of spectral counts (SpC) identifying a protein, divided bythe protein's length (L), divided by the sum of SpC/L for all proteinsin the experiment. NSAF allows the comparison of abundance of individualproteins in multiple independent samples and has been applied toquantify the expression changes in various complexes.

In the present invention, to measure enrichment of a protein, thenormalized spectral abundance factor (NSAF) is calculated for eachprotein in each lane of an SDS-PAGE gel by dividing the number ofspectral counts (normalized for the size of the protein) of a givenprotein by the sum of all normalized spectral counts of all proteins inthe gel lane. The enrichment level for each protein is identified bycalculating the fold enrichment (tagged chromatin/untagged chromatin)using the NSAF values. In an exemplary embodiment, proteins enriched ina sample containing a tagged target chromatin compared to a samplecontaining an untagged target chromatin are enriched by at least about 2fold. In other embodiments, proteins enriched in a sample containing atagged target chromatin compared to a sample containing the untaggedtarget chromatin are enriched by at least about 1.5 fold. In otherembodiments, proteins enriched in a sample containing a tagged targetchromatin compared to a sample containing an untagged target chromatinare enriched by at least about 3 fold, about 4 fold, about 5 fold, about6 fold, about 7 fold, about 8 fold, about 9 fold, about 10 fold, about11 fold, about 12 fold, about 13 fold, about 14 fold, about 15 fold,about 16 fold, about 17 fold, about 18 fold, about 19 fold or about 20fold. As such, a protein enriched by at least about 2 fold in a taggedchromatin sample compared to an untagged chromatin sample, isspecifically associated with the chromatin. For instance, a baseline fornon-specifically associated proteins may be proteins enriched by lessthan about 1.5 fold in a tagged chromatin sample compared to an untaggedchromatin sample, wherein one or more proteins are not associated withchromatin. Non-limiting examples of proteins not associated with achromatin may include enzymes required for metabolism, receptors, andribosomal proteins. In preferred embodiments, proteins not associatedwith a chromatin are ribosomal proteins, and a baseline fornon-specifically associated proteins is an enrichment less than about1.5 fold in a tagged chromatin sampled compared to an untagged chromatinsample. In an exemplary embodiment, proteins or protein fragmentsenriched by at least 15 fold in a tagged chromatin sample compared to anuntagged chromatin sample are specifically associated with a targetchromatin.

In preferred embodiments, a target chromatin is tagged in one cellsample and a target chromatin is not tagged in a second cell sample, andMS analysis is used to identify proteins or protein fragments isolatedduring affinity purification of each sample, and label-free proteomicsis used to determine if a protein or a protein fragment is specificallyor non-specifically associated with the target chromatin. Methods ofderiving MS data to identify proteins or protein fragments are known inthe art, and may include using known computational techniques to distillMS data such as Mascot Distiller, Rosetta Elucidator, and MaxQuant. Insome embodiments, MS data is derived using Rosetta Elucidator. In otherembodiments, MS data is derived using MaxQuant. In preferredembodiments, MS data is derived using Mascot Distiller.

IV. Applications

A method of the invention may be used for any application wherein adetermination of chromatin structure or function may be required. Forinstance, a method of the invention may be used to determinerearrangement in chromatin structure, genome metabolism, epigeneticregulatory mechanisms, transient association of proteins with chromatin,initiation or silencing of expression of a nucleic acid sequence,identify proteins transiently associated with a chromatin, orpost-translational modification of proteins associated with a chromatinor chromatin rearrangement. An application of a method of the inventionmay include determining changes in chromatin function and structure inresponse to changing growth conditions, exposure to a drug or smallmolecule, or during stages of cell cycles.

A method of the invention may also be used to determine proteinslocalized to a target chromatin associated with a specific diseasestate. For example, a biological sample may be obtained from a subjectwith a specific disease and a biological sample may be obtained from asubject without a specific disease. A method of the invention may beperformed on each of the biological samples. The difference in proteinsassociated with the target chromatin between the disease sample and thenon-disease sample may then be compared. Such a method allows thedetermination of proteins localized to a target chromatin associatedwith a specific disease state. In certain embodiments, the disease maybe cancer. The information gleaned from the foregoing method may be usedto identify potential targets for drug development.

Additionally, a method of the invention may be used to diagnose adisease. For example, a biological sample may be obtained from a subjectsuspected of having a specific disease. A method of the invention may beperformed on the biological sample. The identification of proteinsspecifically associated with a target chromatin may be compared to areference sample, wherein when the reference sample is from a diseasedsubject, the proteins specifically associated with a target chromatinare the same or wherein when the reference sample is from a non-diseasedsubject, the proteins specifically associated with a target chromatinare different, then the subject may be diagnosed with the disease.

Further, a method of the invention may be used to map the 4Darchitecture of chromatin. Accordingly, a method of the invention may beused to study regions of chromosomes that come in contact with eachother. Additionally, a method of the invention may be used to understandthe proteins involved in chromosomal architecture.

In some embodiments, a method of the invention is used to determinedifferences in chromatin structure and function between atranscriptionally silent and a transcriptionally active state of agenomic locus. As such, proteins specifically associated with a genomiclocus, and post-translational modifications of proteins associated witha chromatin comprising the genomic locus may be determined in cellscomprising a transcriptionally silent state of a genomic locus, and incells comprising a transcriptionally active state of a genomic locus.

V. Kits

In other aspects, the present invention provides kits for isolating andidentifying proteins specifically associated with a chromatin. The kitsmay comprise, for example, a growth medium comprising a metabolic label,or a metabolic label that may be added to a growth medium, and cellscomprising a tagged target chromatin, and instructions describing amethod of the invention. A kit may further comprise material necessaryfor affinity purification of a tagged target chromatin, and a samplecomprising metabolically labeled and unlabeled non-specificallyassociated proteins for determination of a baseline for non-specificallyassociated proteins. A kit my also comprise material necessary foraffinity purification of a tagged target chromatin, and instructionsdescribing a method of the invention.

In other embodiments, a kit may comprise a protein A-tagged TAL proteinengineered to bind a target chromatin. In alternative embodiments, a kitmay comprise a vector for expressing a protein A-tagged TAL protein,wherein the TAL protein may be engineered to bind a target chromatin.

In still other embodiments, a kit may comprise an affinity handle-taggedinactivated Cas9 and gRNA engineered to bind a target chromatin. A kitmay comprise nucleic acids suitable for expressing an affinityhandle-tagged inactivated Cas9 and gRNA engineered to bind a targetchromatin or cells comprising nucleic acids suitable for expressing anaffinity handle-tagged inactivated Cas9 and gRNA engineered to bind atarget chromatin. A kit may also comprise instructions for expressingand purifying an affinity handle-tagged inactivated Cas9 and gRNAengineered to bind a target chromatin. In each of the foregoingembodiments, a kit may further comprise an affinity handle-taggedinactivated Cas9 without a gRNA for use as a control.

Cells and methods of the invention may be as described in Section I,Section II, and Section III above.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Introduction for Examples 1-3

It has long been appreciated that chromatin-associated proteins andepigenetic factors play central roles in cell-fate reprogramming ofgenotypically identical stem cells through lineage-specifictranscription or repression of precise genes and large chromosomalregions (Martin, 1981; Ho and Crabtree, 2010; Rossant, 2008). However,the hierarchy of chromatin-templated events orchestrating the formationand inheritance of different epigenetic states remains poorly understoodat a molecular level. Since misregulation of chromatin structure andpost-translational modification of histones (PTMs) is linked to cancerand other epigenetic diseases (Jones and Baylin, 2007; Chi et al.,2010), it is imperative to establish new methodologies that will allowcomprehensive studies and unbiased screens for participants inepigenetic mechanisms. Unfortunately, defining how chromatin regulatorscollectively assemble and operate on a precise region of the genome isdifficult to elucidate; there are no current methodologies that allowfor determination of all proteins present at a defined, small region ofchromatin.

Technical challenges have precluded the ability to determine positioningof chromatin factors along the chromosome. Chromatin immunoprecipitation(ChIP) assays have been used to better understand genome-widedistribution of proteins and histone modifications within a genome atthe nucleosome level (Dedon at al., 1991; Ren et al., 2000; Pokholok etal., 2005; Robertson et al., 2007; Johnson et al., 2007; Barski at al.,2007; Mikkelsen et al, 2007). However, major drawbacks of ChIP-basedchromatin enrichment methods include experiments that are largelyconfined to examining singular histone PTMs or proteins rather thansimultaneous profiling of multiple targets, the inability to determinethe co-occupancy of particular histone PTMs, and that ChIP is reliant onthe previous identification of the molecular target. Affinitypurification approaches have been devised for the isolation of achromatin region (Griesenbeck et al., 2003; Agelopoulos et al., 2012);however, these approaches were not done at a level for proteomicanalysis and they do not provide a mechanism for determining thespecificity of protein interactions. More recently, groups biochemicallyenriching for intact chromatin have reported characterization ofproteins associated with large chromatin structures such as telomeres(Dejardin and Kingston, 2009) and engineered plasmids (Akiyoshi el al.,2009; Unnikrishnan et al., 2010); however, these approaches do notenrich for a small integrated genomic locus and do not employspecialized mass spectrometric techniques to detect proteincontamination in purified material.

We sought to compare differences in chromatin between thetranscriptionally active and silent states of a single genomic locus,and developed a technology, called chromatin affinity purification withmass spectrometry (ChAP-MS). ChAP-MS provides for the site-specificenrichment of a given ˜1,000 base pair section of a chromosome followedby unambiguous identification of both proteins and histone PTMsassociated with this chromosome section using highly selective massspectrometry. Using ChAP-MS, we were able to purify chromatin at theSaccharomyces cerevisiae GAL.1 locus in transcriptionally silent andactive states. We identified proteins and combinatorial histone PTMsunique to each of these functional states and validated these findingswith ChIP. The ChAP-MS technique will greatly improve the field ofepigenomics as an unbiased approach to study regulatory mechanisms onchromatin.

Example 1 ChAP-MS Technology

FIG. 1A provides an overview of the ChAP-MS approach that was used toscreen for proteins and histone PTMs associated with a specific genomiclocus in transcriptionally active or repressive states. A LexA DNAbinding site was engineered immediately upstream of the GAL1 start codonin a S. cerevisiae strain constitutively expressing a LexA-Protein A(LexA-PrA) fusion protein. The LexA DNA binding site directs thelocalization of the LexA-PrA protein affinity “handle” to the GAL1promoter in vivo. The positioning of the LexA DNA was designed tospecifically enrich for chromatin-associated proteins and histone PTMsregulating gene expression near the transcriptional start site of GAL1.This strain was cultured in glucose to repress gene transcription, orgalactose to activate gene transcription. Following in vivo chemicalcrosslinking to preserve the native protein-protein interactions at GAL1promoter chromatin, the chromatin was sheared to ˜1,000 base pairsections. The PrA moiety of the LexA-PrA fusion protein was then used toaffinity purify the ˜1,000 base pair section of chromatin at the 5′ endof the GAL1 gene for high resolution mass spectrometric identificationof proteins and histone PTMs. It was anticipated that culturing thesecells in glucose would result in the isolation of proteins and PTMscorrelated to silent chromatin, while culturing cells in the presence ofgalactose would purify histone PTMs and proteins, like RNA polymerase,that are involved with active gene transcription.

The GAL1 gene is present at one copy per haploid cell; due to therelative low abundance of the targeted chromatin region in cellularlysates, it was fully anticipated that proteins nonspecificallyassociating with GAL1 chromatin would complicate analysis of theresulting purified material. Copurification of nonspecificallyassociating proteins is one of the major complications of affinitypurifications; however, isotopic labeling of media provides a means togauge in vivo protein-protein interactions and quantitate differences inpeptide abundance (Smart et al., 2009; Tackett et al., 2005a). Theinventors had previously developed a variation of this labelingtechnique called iDIRT (isotopic differentiation of interactions asrandom or targeted) that provides a solution for determining whichcoenriched proteins are specifically or nonspecifically associated witha complex of proteins (Smart et al., 2009; Tackett et al., 2005a). TheiDIRT technique was adapted (as described in FIG. 1B) to control forproteins nonspecifically enriching with LexA-PrA and the resin. By usingthis adaptation of iDIRT on chromatin enriched from active and repressedchromatin states, the proteins nonspecifically enriching with theisolated GAL1 chromatin section were identified. The strain containingthe LexA DNA binding site and LexA-PrA fusion protein was cultured inisotopically light media, while a strain lacking the LexA DNA bindingsite (but still containing the LexA-PrA fusion protein) was cultured inisotopically heavy media (¹³C₆ ¹⁵N₂-lysine). Following isolation of thecells, the light and heavy strains were mixed and colysed. The growthand mixing of light/heavy strains was performed separately under glucoseand galactose growth conditions. The affinity purification of the GAL1chromatin was performed from this mixture of light/heavy lysates.Proteins and histone PTMs specifically associated with the GAL1chromatin containing the LexA DNA binding site were isotopically lightas they arose from the cells grown in light media. Proteins that werenonspecific to the purification were a 1:1 mix of light and heavy asthey were derived equally from the light and heavy lysates. Analysis ofpeptides from the enriched proteins with high-resolution massspectrometry was used to determine the level of isotopically light andheavy proteins, thereby determining whether the detected protein waseither a specific in vivo constituent of GAL1 chromatin or a nonspecificcontaminant.

Example 2 Affinity Purification of a Specific Chromosome Section

To provide for enrichment of a specific chromosome section, a DNAaffinity handle was engineered at the GAL1 gene in S. cerevisiae (FIG.2A). A LexA DNA binding site was inserted via homologous recombinationjust upstream of the GAL1 start codon to create strain LEXA::GAL1. Tocreate this strain, GAL1 was genomically deleted with URA3 in the W303abackground, and then the GAL1 gene was reinserted with the upstream LEXADNA sequence by homologous recombination. A plasmid constitutivelyexpressing LexA-PrA was introduced into the strain to create LEXA::GAL1pLexA-PrA (FIG. 2A). This strain provides a DNA affinity handle at theGAL1 gene and a protein affinity handle for specific enrichment. Todetermine if insertion of this LexA DNA binding site at GAL1 affectedgene transcription, LEXA::GAL1 pLexA-PrA was cultured in glucose torepress gene transcription at GAL1, and separately in galactose toactivate transcription. From these growths, cDNA was prepared andreal-time PCR was used to measure the activation of GAL1 transcriptionin the presence of galactose (FIG. 2B). Insertion of the LexA DNAbinding site just upstream of the GAL1 start codon did not drasticallyaffect the activation of gene transcription; thus, this strain was usedfor ChAP-MS purification of GAL1 chromatin in the transcriptionallyactive and silent states.

To determine the effectiveness of isolation of GAL1 chromatin, thestringency and specificity of different purification conditions wasanalyzed. Purification of protein complexes under increasingstringencies such as high salt levels provides for the isolation offewer nonspecifically interacting proteins (Smart et al., 2009; Tavernaet al., 2006). Since the proteins purified with GAL1 chromatin will bechemically crosslinked, the stringency of the purification canpotentially be quite high. Indeed, ChIP-qPCR against GAL1 showed thatthe PrA-based purification can survive relatively stringent conditions(FIG. 3A). From these studies, 1M NaCl and 1M urea were selected forfuture purifications, as these conditions are quite stringent andprovide for enrichment of the GAL1 chromatin. Using an identical ChIPapproach, the specificity of the GAL1 chromatin enrichment wasdetermined (FIG. 3B). Using primers targeted to the indicated regions ofchromatin surrounding GAL1, it was detected that the first 1,000 basepair section of the GAL/gene was indeed enriched. Enrichment of GAL1chromatin was observed at a similar level under glucose and galactosegrowth conditions (FIG. 3C). The slightly less efficient isolation undergalactose growth conditions may reflect availability of the DNA affinitysite due to alterations in chromatin structure.

Example 3 ChAP-MS Analysis of Transcriptionally Active Anti Silent GAL1Chromatin

Strain LEXA::GAL1 pLexA-PrA was subjected to the ChAP-MS procedure asoutlined in FIG. 1. Strain LEXA::GAL1 pLexA-PrA was grown inisotopically light media, while strain pLexA-PrA was grown inisotopically heavy media. Following growth of each strain to mid-logphase, the cells were treated with 1.25% formaldehyde to trap proteininteractions on the chromosomes. A detailed analysis of the amount offormaldehyde crosslinking required to preserve the in vivo state ofchromatin during affinity purifications was recently published by theinventors (Byrum et al., 2011a, 2011b). Approximately 2.5×10¹¹LEXA::GAL1 pLexA-PrA cells were mixed with an equivalent amount ofisotopically heavy pLexA-PrA cells (separately for media containingglucose and galactose) and then subjected to lysis under cryogenicconditions with a Retch MM301 ball mill (Tackett et al., 2005a). Lysateswere suspended in 20 mM HEPES (pH 7.4), 0.1% Tween 20, 1 M NaCl, 1 Murea, and 2 mM MgCl₂. Lysates were then subjected to sonication andchromatin was sheared to sections of ˜1,000 base pairs. LexA-PrA wascollected on IgG-coated Dynabeads and coenriching proteins were resolvedby SDS-PAGE and visualized by Coomassie staining (FIG. 4A). Gel laneswere sliced into 2 mm sections and subjected to in-gel trypsin digestion(Smart et al., 2009; Tackett et al., 2005a, 2005b). Peptides fromproteins were identified by high-resolution mass spectrometry with aThermo Velos Orbitrap mass spectrometer equipped with a WatersnanoACQUITY UPLC system. Proteins and PTM-containing peptides wereidentified and the level of isotopically light to heavy peptide wascalculated with Mascot Distiller (Smart et al., 2009), Representativespectra are shown in FIG. 4B-D. Major bands observed in the gel lanescorrespond to the affinity purification protein LexA-PrA and IgG chainsas anticipated. Other proteins identified correspond to specifically andnonspecifically enriched proteins. Tables 1 and 2 list the proteinsidentified and percent isotopically light peptides (352 proteins fromthe glucose ChAP-MS and 399 proteins from the galactose ChAP-MS).

Once proteins were identified, a baseline was established fornonspecifically associated proteins in accordance to the iDIRT approach(Smart et al., 2009). Nonspecifically enriching ribosomal proteins wereused to establish the nonspecifically associating baseline (Smart etal., 2009). The average percent isotopically light peptides from 20ribosomal proteins from the glucose and galactose growth conditions wereused to establish this nonspecifically associating baseline (Table 3).This resulted in a nonspecifically associating baseline of 49.93%±2.12%light for the glucose ChAP-MS and 66.8%±7.1% light for the galactoseChAP-MS (FIG. 5). Proteins were categorized as specifically associatingwith GAL1 chromatin if the percent light was greater than 2 SDs abovethe ribosomal level (Smart et al., 2009). FIG. 5 shows the proteins andhistone PTMs specifically enriched with GAL1 chromatin under glucose andgalactose growth conditions. Tables 4 and 5 list proteins that wereidentified as specifically enriched in both the glucose and galactoseChAP-MS analyses. Specifically enriched proteins or histone PTMs knownto be involved in transcriptional regulation are listed in FIG. 5. Forthe glucose and galactose ChAP-MS analyses, 11 and 17 (respectively)additional proteins were detected as specifically enriched (FIG. 5,Tables 4 and 5). These additional proteins are abundant metabolic andheat shock proteins that are typical contaminants and false positivesfor this study. However, narrowing down 352 proteins identified from theglucose ChAP-MS and 399 proteins from the galactose ChAP-MS to 12proteins and 27 proteins/PTMs specifically enriched produced a shortlist of candidates that was easily validated.

The ChAP-MS analyses of GAL1 chromatin revealed association of Gal3,Spt16, Rpb1, Rpb2, H3K14ac, H3K9acK14ac, H3K18acK23ac, H4K5acK8ac, andH4K12acK16ac under transcriptionally active conditions, whiletranscriptionally repressive conditions showed the enrichment ofH3K36me3. In order to validate the ChAP-MS approach, standard ChIP wasperformed to specific interactions detected in the transcriptionallyactive and silent chromatin state at GAL1 (FIG. 6). These ChIPexperiments validated the proteins and PTMs found associated with thetranscriptionally active and repressed states of GAL1 chromatindetermined from the ChAP-MS approach.

Discussion for Examples 1-3

The chromatin biology and epigenomics research communities have beenlimited to biased technologies that restrict targeted genomelocalization studies to previously identified proteins or histone PTMs.Here, a newly developed technology, called ChAP-MS, is described thatcircumvents this limitation by providing for isolation of a ˜1,000 basepair section of a chromosome for proteomic identification ofspecifically bound proteins and PTMs. In essence, the ChAP-MS approachallows one to take a “molecular snapshot” of chromatin dynamics at aspecific genomic locus. Furthermore, employing this approach to targetother chromatin regions will likely provide unprecedented insight on avariety of epigenetic regulatory mechanisms, chromatin structure, andgenome metabolism.

Validation of the ChAP-MS Approach

The ChAP-MS approach was validated on the well-studied GAL1 locus in S.cerevisiae. The GAL1 gene is activated for gene transcription in thepresence of galactose, while glucose represses transcription.Accordingly, it was rationalized that a purified ˜1,000 base pairsection of chromatin at the 5′ end of the GAL1 gene from cells grown ingalactose would contain histone PTMs correlated with activetranscription and cellular machinery necessary for transcription, whilethe same chromatin section from cells grown in glucose would be enrichedwith histone PTMs associated with transcriptional repression. Priorpublications have documented that H3 acetylation is enriched on the 5′end of the active galactose-induced GAL1 gene, while in the presence ofglucose it contains H3K36me3 (Shukla et al., 2006; Houseley et al.,2008). Results presented in the Examples herein with ChAP-MS, supporteach of these prior findings (FIG. 5). Furthermore, the presence ofdoubly acetylated histones (H3K9acK14ac, H3K18acK23ac, H4 K5acK8ac,H4K12acK16ac) during transcriptional activation was identified. Thisdemonstrates how ChAP-MS may be used to study the combinatorial “code”of histone modifications at given chromosome regions without the needfor prior identification of PTMs, PTM-specific antibodies, or sequentialchromatin put-downs. Considering H4K12acK16ac for example, theidentification of the double acetylation is unique to the ChAP-MSapproach as antibodies to this double acetylation do not exist, thus onecould not have performed a biased ChIP analysis. Additionally, it hasbeen reported that commercially available antibodies to singleacetylation at H4K12 or H4K16 are cross-reactive with other H4acetylations and that double acetylation of H4K12K16 significantlyalters the specificity of the antibody to the singly acetylated sites(Bock et al., 2011)—a limitation specific to antibodies used in biasedChIP studies and not to the unbiased ChAP-MS approach that usesquantitative mass spectrometric readout. The ChAP-MS approachsimultaneously identified the presence of RNA polymerase (Rpb1, Rpb2)and FACT component Spt16 (which aids in reorganizing chromatin for RNApol activity) under these transcriptionally active conditions. Also ofinterest was the identification of Gal3 at actively transcribing GAL1,which has previously been shown to inhibit the repressive activity ofGal80 at the GAL10/GAL1 locus (Platt and Reece, 1998). It wasdemonstrated how the ChAP-MS approach may be utilized to study chromatindynamics at GAL1 under different states of gene transcription. Ofparticular interest for future functional studies may be the upstreamactivating sequence which binds the Gal4 actuator and Gal80 repressorwhich may allow better understand of the events surrounding the switchfrom repression to activation at GAL1 and GAL10, as well as the middleand 3′ end of GAL1 to understand the processes of elongation andtermination, respectively.

Utility of ChAP-IViS as a General Tool for Studying Chromatin Biology

The ChAP-MS technology presented here demonstrates the ability to purifya unique chromosome section on the order of four to five nucleosomes inlength from an in vivo source that can subsequently be subjected tosensitive proteomic studies. ChAP-MS has numerous advantages relative totraditional ChIP, including the ability to unbiasedly detectproteins/PTMs at a specific genomic locus and the identification ofcombinatorial histone modifications on a single histone molecule.Furthermore, ChAP-MS only requires approximately an order of magnitudemore cells relative to biased ChIP studies, which is a huge advantage ifdoing more than ten blind ChIP studies at a given region is factored in(chances are many antibodies for many proteins would be heavily investedin, trying to guess a specifically bound protein/PTM). In this regard,ChAP-MS is a more cost-effective option for characterizing specificallybound proteins and histone PTMs relative to ChIP. Future derivations ofthis technology may employ targeted mass spectrometric approaches forbetter determination of combinatorial histone PTMs as well asidentification of other regulatory PTMs on nonhistone proteins fromthese isolated sections (Taverna et al., 2007). Given the sensitivity ofthe mass spectrometry analysis employed and the relatively modestbiological starting material, the findings presented in the Examplesherein also establish a framework for applying ChAP-MS to profile acrossentire regions of chromosomes or investigate higher eukaryotic systems.Regardless, any advances that permit ChAP-MS analysis of in vivountagged or unaltered samples, like tissues, will undoubtedly havevaluable applications for investigating altered gene transcriptionmechanisms in human disease states, as this technique could provide acomprehensive way to intelligently identify targets for therapeutics.

Experimental Procedures for Examples 1-3 Construction of the LEXA::GAL1pLexA-PrA Strain

The LEXA::GAL1 pLexA-PrA strain used to affinity enrich GAL1 chromatinwas designed to have a LexA DNA binding site just upstream of the GAL1start codon and contains a plasmid constitutively expressing a LexA-PrAfusion protein. In S. cerevisiae from the W303a background, the GAL1gene was genomically replaced with URA3 using homologous recombination.Next, the GAL1 gene (+50 base pairs up- and downstream) was PCRamplified with primers that incorporated a LexA DNA binding site(5′-CACTTGATACTGTATGAGCATACAGTATAATTGC) immediately upstream of the GAL1start codon. This LEXA::GAL1 cassette was transformed into thegal1::URA3 strain and selected for growth with 5-fluoroorotic acid,which is lethal in URA3 expressing cells. Positive transformants weresequenced to ensure homologous recombination of the cassette to createthe LEXA::GAL1 strain. A plasmid that constitutively expresses LexA-PrAfusion protein with TRP selection was created by amplification of thePrA sequence from template pOM60 via PCR and subcloning into theSac1/Sma1 ends of the expression plasmid pLexA-C. Transforming thisplasmid into the LEXA:GAL1 strain gave rise to the LEXA:GAL1 pLexA-PrAstrain. Additionally, a control used in these studies was W303a S.cerevisiae transformed only with pLexA-PrA.

Cell Culture

Strains LEXA:GAL1 pLexA-PrA and pLexA-PrA were grown in yeast syntheticmedia lacking tryptophan to mid-log phase at 30° C. LEXA:GAL1 pLexA-PrAstrain growths were done with isotopically light lysine, while strainpLexA-PrA was cultured exclusively with isotopically heavy ¹³C6¹⁵N₂-lysine. For each strain, 12 l of media containing either 2% glucoseor 3% galactose were grown to yield ˜5×10¹¹ cells per growth condition.At mid-log phase, the cultures were crosslinked with 1.25% formaldehydefor 5 min at room temperature and then quenched with 125 mM glycine for5 min at room temperature. Cells were harvested by centrifugation(2,500×g) and frozen in liquid nitrogen as pellets in suspension with 20mM HEPES (pH 7.4), 1.2% polyvinylpyrrolidone (1 ml/10 g of cell pellet).Frozen cell pellets were mixed as follows at 1:1 cell weight ratios: (1)LEXA:GAL1 pLexA-PrA isotopically light in glucose plus pLexA-PrAisotopically heavy control in glucose (2) LEXA:GAL1 pLexA-PrAisotopically light in galactose plus pLexA-PrA isotopically heavycontrol in galactose. Cell mixtures were cryogenically lysed underliquid nitrogen temperature with a Retsch MM301 ball mill (Smart et al.,2009; Tackett et al., 2005a).

ChAP-MS Procedure

Each of the following two cell lysates were processed for purificationof GAL1 chromatin: (1) LEXA:GAL1 pLexA-PrA isotopically light in glucoseplus pLexA-PrA isotopically heavy control in glucose, referred to as theglucose ChAP-MS, and (2) LEXA:GAL1 pLexA-PrA isotopically light ingalactose plus pLexA-PrA isotopically heavy control in galactose,referred to as the galactose ChAP-MS. Twenty grams of frozen cell lysate(˜5×10¹¹ cells) was used for each of the glucose and galactose ChAP-MSanalyses. ChAP-MS steps were performed at 4° C. unless otherwise noted.Lysates were resuspended in 20 mM HEPES (pH 7.4), 1 M NaCl, 2 mM MgCl₂,1 M urea, 0.1% Tween 20, and 1% Sigma fungal protease inhibitor cocktailwith 5 ml buffer per gram of frozen lysate. Lysates were subjected tosonication with a Diagenode Bioruptor UCD-200 (low setting, 30 s on/offcycle, 12 min total time) in 20 ml aliquots to yield ˜1 kb chromatinfragments. Supernatants from sonicated lysates were collected bycentrifugation at 2,000×g for 10 min. Dynabeads (80 mg) coated withrabbit IgG were added to the lysates and incubated for 4 hr withconstant agitation (Byrum et al., 2012a). Dynabeads were collected witha magnet and washed 5 times with the purification buffer listed aboveand 3 times with 20 mM HEPES (pH 7.4), 2 mM MgCl₂, 10 mM NaCl, 0.1%Tween 20. Washed Dynabeads were treated with 0.5 N ammoniumhydroxide/0.5 mM EDTA for 5 min at room temperature to elute proteins.Eluants were lyophilized with a Savant SpeedVac Concentrator.Lyophilized proteins were resuspended in Laemmli SDS-PAGE loadingbuffer, heated to 95° C. for 20 min, resolved with 4%-20% tris-glycineInvitrogen precast gels, and visualized by colloidal Coomassie staining.

High-Resolution Mass Spectrometry and Data Analysis

Gel lanes were sliced into 2 mm sections and subjected to in-gel trypsindigestion (Byrum et al., 2011a, Byrum et al., 2011b, Byrum et al.,2012a; Tackett et al., 2005b). Peptides were analyzed with a ThermoVelos Orbitrap mass spectrometer coupled to a Waters nanoACQUITY liquidchromatography system (Byrum et al., 2011b). Using a data-dependentmode, the most abundant 15 peaks were selected for MS² from ahigh-resolution MS scan. Proteins were identified and the ratio ofisotopically light/heavy lysine-containing tryptic peptide intensity wasdetermined with Mascot and Mascot Distiller. The search parametersincluded: precursor ion tolerance 10 ppm, fragment ion tolerance 0.65Da, fixed modification of carbamidomethyl on cysteine, variablemodification of oxidation on methionine, and two missed cleavagespossible with trypsin. A threshold of 95% confidence for proteinidentification, 50% confidence for peptide identification and at leasttwo identified peptides per protein was used, which gave a 2% peptidefalse discovery rate. All specifically associating proteinidentifications and ratios were manually validated.

A baseline was established for nonspecifically associated proteins withnonspecifically enriched ribosomal proteins (Smart et al., 2009). Theaverage percent isotopically light peptides from 20 ribosomal proteinsfrom the glucose and galactose growth condition were used to establishthis nonspecifically associated baseline. This resulted in anonspecifically associated baseline of 49.93%±2.12% light for theglucose ChAP-MS and 66.8%±7.1% light for the galactose CHAP-MS. Proteinswere categorized as specifically associating if the percent light wasgreater than 2 SDs above the ribosomal level (Tables 4 and 5) (Smart etal., 2009). Duplicate ChAP-MS procedures showed Pearson and Spearmancorrelation coefficient p values of <0.001.

ChIP and Gene Transcription Assays

ChIP and gene transcription assays were performed as previously reported(Tackett et al., 2005b; Taverna et al., 2006). Assays were performed intriplicate and analyzed by real time PCR.

Introduction for Examples 4-5

One of the most compositionally diverse structures in a eukaryotic cellis a chromosome. A multitude of macromolecular protein interactions andepigenetic modifications must properly occur on chromatin to drivefunctional aspects of chromosome biology like gene transcription, DNAreplication, recombination, repair and sister chromatid segregation.Analyzing how proteins interact in vivo with chromatin to direct theseactivities and how epigenetics factors into these mechanisms remains asignificant challenge owing to the lack of technologies tocomprehensively analyze protein associations and epigenetics at specificnative chromosome sites. Chromatin immunoprecipitation (ChIP) assayshave traditionally been used to better understand genome-widedistributions of chromatin-associated proteins and histonepost-translational modifications (PTMs) at the nucleosome level (Cermaket al., 2011). However, major drawbacks of current ChIP-based methodsinclude their confinement to examining singular histone PTMs or proteinsrather than simultaneous profiling of multiple targets, the inability ofChIP to directly determine the co-occupancy of particular histone PTMsand that ChIP is reliant on the previous identification and developmentof affinity reagents against the molecular target. A more comprehensiveand unbiased approach would be the biochemical isolation of a specificnative genomic locus for proteomic identification of proteins-associatedand histone PTMs. Similar approaches have been performed for largestructures like telomeres, engineered plasmids or engineered loci(Griesenbeck et al., 2003; Dejardin and Kingston, 2009; Hoshino andFuji, 2009; Akiyoshi et al., 2009; Unnikrishnan et al., 2010; Byrum etal., 2012b); however, the proteomic analysis of a small native genomicregion without genomic engineering has yet to be performed. To worktoward proteomic studies of native chromatin regions (i.e. sections ofchromatin that are unaltered genetically and spatially the genome), werecently developed a technique termed Chromatin Affinity Purificationwith Mass Spectrometry (ChAP-MS) that provides for the enrichment of anative 1-kb section of a chromosome for site-specific identification ofprotein interactions and associated histone PTMs (Byrum et al., 2012b).This ChAP-MS approach uses the association of an ectopically expressedaffinity-tagged LexA protein with a genomically incorporated LexA DNAbinding site for site-specific chromatin enrichment. The ChAP-MSapproach provides for the isolation of chromatin from the native site inthe chromosome; however, one must genomically engineer a LexA DNAbinding site, which could alter the native state of the chromatin andwhich requires a biological system readily amendable to genomicengineering.

To alleviate genomic engineering for affinity enrichment of chromatinsections, we report the use of modified transcription activator-like(TAL) effector proteins to site-specifically target a native section ofa chromosome for purification and proteomic analysis. We term thisapproach TAL-ChAP-MS (FIG. 7A). TAL effector proteins are fromXanthomonas, which infects plants and translocates TAL effectors intocells where they serve as transcription activators (Scholze and Boch,2010; Scholze and Boch, 2011; Doyle et al., 2012). TALs contain acentral domain of 18 tandem repeats of 34 amino acids each, which directsequence-specific DNA binding (Doyle et al., 2012; Cermak et al., 2011).Binding to a given nucleobase in DNA is determined by two adjacent aminoacids (12 and 13) within each of the 18 repeats (Scholze and Boch,2010). Thus, by mutating these amino acids in each of the 18 tandemrepeats, one can ‘program’ binding to a given 18-nt region of DNA invivo. TAL proteins have been validated in cell culture for targetingnucleases for genome editing and for targeting transcription activators(Miller et al., 2011; Geissler et al., 2011). To test the ability of aTAL protein to serve as an affinity enrichment reagent for nativechromatin isolation, a TAL protein was designed that bound a unique18-nt region of DNA in the promoter region of the GAL1 gene inSaccharomyces cerevisiae (FIG. 7B). We chose to analyze proteins andhistone PTMs regulating the galactose-induced gene transcription of GAL1because (1) this is a well-studied genomic locus, which will provide forproof-of-principle analysis, and (2) we previously used this locus todevelop the ChAP-MS technique (Byrum et al., 2012b); thus, a comparisoncan be made to the new TAL-ChAP-MS approach.

One of the major complications for studying specific proteinassociations with purified protein complexes or with chromatin is theco-enrichment of non-specifically associating proteins. Thisparticularly becomes an issue when studying low copy number entitiessuch as a single genomic locus. With the advancement of high-resolutionand sensitive mass spectrometry in recent years, it has been suggestedthat >10⁹ cell equivalents are needed to study single genomic loci withproteomic approaches (Chait, 2011). In agreement, our ChAP-MS studiesused 10¹¹ cells for isolation of GAL1 promoter chromatin at levelssufficient for proteomic analysis (Byrum et al., 2012b). When scaling uppurifications of low copy entities to meet the sensitivity necessary forhigh-resolution mass spectrometric analysis, the issue of co-purifyingabundant non-specific proteins becomes a major challenge. In the ChAP-MSapproach (Byrum et al., 2012b), we used an isotope-labeling strategy tocategorize whether a protein co-enriching with a section of chromatinwas specifically associated or a contaminant. Limitations forisotope-labeling approaches are cost and having biological systems ofstudy that are amendable to stable isotope-labeling with amino acids. Tocircumvent the use of isotope-labeling, we now have incorporatedlabel-free quantitative mass spectrometry in the TAL-ChAP-MS workflow.The described TAL-ChAP-MS approach can therefore provide for thepurification of a native chromatin region for label-free quantitativeproteomic analysis, which will greatly simplify studies of how proteinsand combinatorial histone PTMs regulate chromosome metabolism.

Example 4 Development of TAL-ChAP-MS

A schematic of the TAL-ChAP-MS approach to purify native chromatin forproteomic analysis is shown in FIG. 7A. To demonstrate the utility ofthe TAL-ChAP-MS approach, we used a TAL protein to target the promoterchromatin region upstream of the galactose-inducible GAL1 gene in S.cerevisiae (FIG. 7B). Yeast cells were grown in the presence ofgalactose to induce transcription of the GAL1 gene, which will recruitproteins and histone PTMs that activate transcription. A wild-typeculture and a culture of cells containing a plasmid that expressed aPrA-tagged TAL protein that bound the GAL1 promoter region were grownand subjected to in vivo formaldehyde cross-linking to preservechromatin structure during purification (Byrum et al., 2011a; Byrum etal., 2011b). Following cryogenic cell lysis and sonication of chromatinsections to ˜1 kb, each lysate was independently subjected to affinityenrichment of PrA with IgG-coated Dynabeads. Proteins co-enriching withTAL-PrA from the cells containing the pTAL-PrA plasmid and thoseenriching as contamination from the control cells with no plasmid wereidentified by high-resolution mass spectrometry. Using label-freequantitative analyses, the relative enrichment of proteins and histonePTMs specifically hound to the GAL1 promoter chromatin were identified.

Saccharomyces cerevisiae cells were transformed with pTAL-PrA, andprotein expression was validated by western blotting (FIG. 7C). Toevaluate whether TAL-PrA expression affected galactose-inducedtranscription of GAL1, cDNA was prepared from wild-type and wild-type(+pTAL-PrA) cells under glucose (transcriptionally repressed GAL1) andgalactose (transcriptionally active GAL1) growth conditions.Quantitative rtPCR of this cDNA revealed that expression of TAL-PrA didnot affect galactose-induced GAL1 transcription (FIG. 7D). To determinewhether TAL-PrA enriched chromatin at the GAL1 promoter region, ChIP wasperformed to the PrA-tag in cells from glucose and galactose growths(FIG. 7E-G). Under transcriptionally active conditions, TAL-PrAspecifically enriched chromatin from the GAL1 promoter region relativeto sequences 2 kb up- and downstream (FIG. 7F). The level of chromatinenrichment by TAL-PrA under transcriptionally active conditions wassimilar to the level used for proteomic studies with LexA-PrA affinityenrichment in the ChAP-MS approach (Byrum et al., 2012b). Interestingly,the TAL-PrA protein did not show enrichment of the GAL1 promoterchromatin under transcriptionally repressive glucose growth conditions(FIG. 7G). One possibility of many is that the lack of enrichment couldbe due to inaccessibility of the TAL-PrA to the genomic target due toaltered chromatin structure under transcriptionally repressiveconditions—highlighting the importance for measuring specific chromatinenrichment of the TAL protein before using this approach for specificchromatin enrichment. In the previous publication of the ChAP approach(Byrum et al., 2012b), a LexA-PrA was targeted just upstream of thestart codon of GAL1 for enrichment of chromatin, which showed enrichmentunder both glucose and galactose growth conditions. Importantly, the TALused in the current study was targeted 193 bp upstream of the targetsite of LexA, which suggests that proximal regions may be differentiallyaccessible to DNA-binding affinity reagents under varioustranscriptional states. In addition to analyzing enrichment of GAL1chromatin relative to proximal sequences (FIG. 7E-G), enrichment of GAL1chromatin was measured relative to the five most homologous sequences inthe genome (Table 6). The GAL1 target DNA showed 4.6-fold betterenrichment relative to the next five most similar sites in thegenome—demonstrating specificity of the TAL protein used in this studyto the targeted sequence at the GAL1 promoter region. Collectively, thedata in FIG. 7C-G and Table 6 demonstrate that the TAL-ChAP-MS approachcan provide enriched chromatin from the GAL1 promoter undertranscriptionally active conditions that would be suitable for proteomicstudies.

Example 5 Using TAL-ChAP-MS to Identify Proteins and Histone PTMs at theGAL1 Promoter

As detailed in the Experimental Procedures for Examples 4-5 section,chromatin from the transcriptionally active GAL1 promoter was enrichedwith TAL-PrA and resolved by SDS-PAGE (FIG. 8A). The similarCoomassie-stained protein pattern for the TAL-PrA and wild-type controlsamples in FIG. 8A demonstrates that the co-enrichment of contaminatingproteins was a major issue for this approach. Accordingly, thelabel-free spectral counting approach described in the ExperimentalProcedures for Examples 4-5 section was used to identify proteinsspecifically enriched with the TAL-PrA. High-resolution massspectrometry coupled with label-free proteomics was used to identifyproteins and histone PTMs specifically enriched with the GAL1 promoterchromatin (FIG. 8B and Table 7). We focused our analysis on the top 10%of enriched proteins (54 proteins) that each showed >15-fold enrichmentwith the TAL-PrA (Table 7). Four of these 54 proteins (Rpb1, Rpb2, Spt16and Gal3) are involved with active transcription of GAL1, and these arethe same four proteins previously identified at the promoter of GAL1with the ChAP-MS approach (Byrum et al., 2012b). Rpb1 and Rpb2 are RNApolymerise components, and Spt16 is a subunit of yFACT that aids inre-organizing chromatin for RNA polymerase activity. Gal3 has previouslybeen shown to inhibit the repressive activity of Gal80 at GAL1 locus(Platt and Reece, 1998). Rpb1, Rpb2, Spt16 and Gal3 were confirmed to beassociated adjacent to the TAL-PrA genomic binding site with standardChIP (FIG. 8C). Thus, the TAL-ChAP-MS approach identified precisely thesame proteins as the published ChAP-MS approach during transcriptionalactivation at the promoter of GAL1, thereby validating the TAL-ChAP-MSapproach for studying the local proteome of small chromatin regions andthe use of label-free proteomic approaches for quantifying suchenrichments. Many of the other 50 proteins identified as >15-foldenriched with TAL-PrA are typical non-specific protein associationsfound in affinity purifications (e.g. highly abundant metabolic andribosomal proteins).

In addition to protein associations with the GAL1 promoter, thefollowing single histone PTMs were identified under transcriptionallyactive conditions: H3K14ac, H3K56ac, H3K79me1/me2/me3, H2BKI7ac andH2AK7ac; and the following combinatorial histone PTMs: H3K9acK14ac,H3K18acK23ac, H2BK6acK11ac and H2BK11acK17ac (FIG. 8B and Table 8). Thepresence of H3K14ac was confirmed by standard ChIP (FIG. 8C). Previouslyusing ChAP-MS and routine ChIPs (Byrum et al., 2012b), a similar profileof singly acetylated H3 lysine residues was identified at the GAL1promoter region, thus confirming the utility of the TAL-ChAP-MSapproach. In addition to the acetylations observed in the ChAP-MS study,the TAL-ChAP-MS approach additionally identified methylation of H3K79.As previously reported for the ChAP-MS approach, the TAL-ChAP-MSapproach uncovered combinatorial sets (i.e. multiple PTMs on singlepeptides) of histone PTMs under transcriptionally active conditions atthe promoter of GAL1. The use of a technology like TAL-ChAP-MS toidentify previously unknown combinatorial modifications is crucial tounderstand the epigenome, as specific antibodies to combinatorialhistone PTMs are not usually available for standard approaches likeChIP. In general terms, acetylation of histone lysine residues andmethylation of H3K79 correlate to transcriptional activation(Kouzarides, 2007); thus, the histone PTMs uncovered by TAL-ChAP-MScorrelate to the active transcription state of GAL1 in the presence ofgalactose.

Discussion for Examples 4-5

We describe a novel approach called TAL-ChAP-MS that provides for thebiochemical isolation of 1-kb native chromatin sections for proteomicidentification of specifically associated proteins and combinatorialhistone PTMs. The described TAL-ChAP-MS approach overcomes limitationsof the ChAP-MS approach (Byrum et al., 2012b), as genomic engineering isnot necessary for TAL-based affinity enrichment and because proteinenrichment with a given locus can now be determined with label-freeproteomics. Even without genomic engineering of the DNA, the ChAP-MSapproach does require targeting of a DNA-binding affinity enrichmentreagent (i.e. the TAL protein), which has the potential to perturb thechromatin state. However, the data in FIG. 7D demonstrate thattranscription of GAL1 is not altered on TAL targeting, which supportsmaintenance of the chromatin integrity for the studies reported here.Targeting TALs to different sequences in adjacent genomic regions thatwould provide for purification of overlapping chromatin sections is onepossible way for investigators to overcome concerns of TAL binding (i.e.a tiling approach). The implications of the TAL-ChAP-MS approach arefar-reaching as investigators can now begin to elucidate the dynamics ofchromatin regulation in a site-specific and comprehensive manner.Researchers will now only need to ‘reprogram’ the DNA-bindingspecificity of the TAL protein to obtain a unique affinity purificationreagent for their chromosome region of interest. Using the TAL-ChAP-MSapproach brings researchers closer to being able to take molecular‘snapshots’ of the assembly and disassembly of proteins on chromatin andhow epigenetic states are modulated at small genomic loci.

Experimental Procedures for Examples 4-5 pTAL-PrA Plasmid, Real-TimertPCR and ChIP

For affinity enrichment of chromatin from the promoter region of theGAL1 gene in S. cerevisiae, a TAL protein was designed (by the GeneArtPrecision TAL services of Life Technologies) to bind a unique 18-ntsequence (GGGGTAATTAATCAGCGA) 193 base pairs upstream of the GAL1open-reading frame (FIG. 7B). The TAL protein was designed as atruncation that lacked the native N-terminal transcription activationdomain, but it contained the site-specific DNA-binding region. Todevelop an affinity enrichment reagent, the LexA-coding region ofpLexA-PrA [plasmid that constitutively expresses a PrA-tagged LexAprotein under TRP selection; from (Byrum et al., 2012b)] was replacedwith the TAL-coding region to generate pTAL-PrA. Real-time qPCRmeasurement of galactose-induced transcription of GAL1 and all ChIPstudies were performed as reported in (Byrum et al., 2012b).

TAL-ChAP-MS

To test the TAL-ChAP-MS approach at the promoter region of GAL1,wild-type and wild-type (+pTAL-PrA) S. cerevisiae (W303 matA) cells werecultured to mid-log phase in 3% galactose-containing media, subjected to1.25% formaldehyde cross-linking, cryogenically lysed and subjected tosonication to shear genomic DNA to ˜1 kb [as detailed in (Byrum et al.,2012b; Byrum et al., 2011a; Byrum et al., 2011b)]. Immunoglobulin G(IgG)-coated Dynabeads were added to lysate from ˜10¹¹ cells from eachgrowth separately [as detailed in (Byrum et al., 2012b)]. Proteinsco-enriching with the TAL-PrA (wild-type cells +pTAL-PrA lysate) orproteins non-specifically binding to the Dynabeads (wild-type celllysate) were resolved by SDS-PAGE/Coomassie-staining (FIG. 8A), excisedas 2-mm bands from the entire gel lane, digested in-gel with trypsin andsubjected to high-resolution tandem mass spectrometric analysis with aThermo Velos Orbitap mass spectrometer [as reported in (Byrum et al.,2012b)]. Proteins and typical histone PTMs (lysine acetylation andmethylation) were identified using Mascot (Tables 7 and 8). To measureenrichment of a protein, the normalized spectral abundance factor(Zybailov et al., 2006) was calculated for each protein in each lane bydividing the number of spectral counts (normalized for the size of theprotein) of a given protein by the sum of all normalized spectral countsof all proteins in the gel lane (Byrum et al., 2011c). The enrichmentlevel for each protein was identified by calculating the fold enrichment(TAL-PrA/wild type) using the normalized spectral abundance factorvalues (Table 7). Proteins with a fold enrichment >2 (511 of 1459proteins identified) were used to generate a quantile plot of foldenrichment with GAL1 promoter chromatin (FIG. 8B).

Introduction for Example 6

For the work presented, a “local epiproteome” refers to not only thehistone PTMs at a specific chromosomal location that are involved in aparticular activity (Dai and Rasmussen, 2007), but also to the otherproteins associated with the region in addition to the histones.Identifying the components of a specific epiproteome can provideunprecedented insight into the molecular and epigenetic mechanismsregulating an activity. For example, gene transcription could havevarious epiproteomes that regulate initiation, elongation andtermination. A recently realized milestone for measuring localepiproteomes has been the development of affinity enrichment proceduresto isolate small regions of chromatin (Byrum et al., 2013; Byrum et al.,2012b; Dejardin and Kingston, 2009; Akiyoshi et al., 2009; Hoshino andFujii, 2009; Griesenbeck et al., 2003; Unnikrishnan et al., 2010;Hamperl et al., 2014). Purification of a small region of chromatin fromthe cellular milieu is one of the most challenging aspects of theseapproaches as the proteins and histone PTMs specifically isolated withthe targeted chromatin typically constitute a small fraction of theidentified proteins—most of which are non-specific associations (Byrumet al., 2013; Byrum et al., 2012b; Byrum et al., 2011a). We developedtwo approaches using quantitative high resolution mass spectrometry thatdistinguish whether proteins and histone PTMs identified duringepiproteome measurements are “specific” to the target chromatin or are“non-specific” contaminants (Byrum et al., 2013; Byrum et al., 2012b).These quantitative approaches are critical components of our ChAP-MS(Chromatin Affinity Purification with Mass Spectrometry) platform oftechnologies that enable local epiproteome analysis. Included in thisplatform are the first generation ChAP-MS and second generationTAL-ChAP-MS approaches (Byrum et al., 2013; Byrum et al., 2012b). TheChAP-MS approach, which used a targeted LexA protein as an affinityreagent, demonstrated the first unambiguous epiproteome measurement. TheTAL-ChAP-MS approach achieved similar high resolution and specificity byusing the genomic targeting ability of the TALEN (TranscriptionActivator-Like Effector Nuclease) system for local epiproteome isolationand analysis (Byrum et al., 2012b; Scholze and Boch, 2011).

Described here is the third generation technology termed CRISPR-ChAP-MS(FIG. 9). The prokaryotic viral defense system CRISPR (ClusteredRegularly Interspaced Palindromic Repeats) has recently been developedas a genome-editing tool for eukaryotes (Mali et al., 2013). The corecomponents of this system include the Cas9 nuclease, which is able tocreate double-strand breaks in DNA, and guide RNA (gRNA), which is boundby Cas9 and serves to direct this complex to a target sequencecomplementary to the gRNA. Using the Type II CRISPR system from S.pyogenes, we have harnessed the specific gene-targeting capability ofthe Cas9/gRNA complex to isolate and unambiguously identify a specificlocal epiproteome. We created a PrA-tagged version of Cas9 with acatalytically inactive nuclease along with a gRNA to target the promoterregion of the GAL1 gene in S. cerevisiae to validate the CRISPR-ChAP-MStechnology (FIG. 9).

To isolate the targeted chromatin, cells were treated with formaldehydeto stabilize interactions (Byrum et al., 2012b), chromatin was shearedto fragments approximately 1 kb in length, and the target chromatin wasaffinity purified using the PrA tag. Affinity tagged versions of Cas9have been shown to target chromatin for partial enrichment (Fujita andFujii, 2013); however, a quantitative analysis of the specifically boundproteins and histone PTMs has not been reported. Here using ourCRISPR-ChAP-MS approach that does provide for quantitativeidentification of specifically bound proteins and histone PTMs, the GAL1promoter chromatin from yeast was isolated under transcriptionallyactive conditions and subjected to a label-free quantitative massspectrometric workflow to identify the specific components of the localepiproteome. Relative to the first and second generations of the ChAP-MStechnological platform, CRISPR-ChAP-MS shows an enhanced ability toisolate targeted chromatin, which is critical for epiproteome analysis.The TAL-based approach also requires design of a specific TAL proteinfor each sequence targeted whereas CRISPR-ChAP-MS only requiressite-directed mutagenesis to alter the gRNA for genomic targeting, whichprovides a more cost effective approach that can easily be multiplexedto target additional sites.

Example 6 A CRISPR-Based Approach for High Resolution EpiproteomeIdentification

To validate the CRISPR-ChAP-MS approach, the promoter chromatin of theGAL1 gene was targeted for enrichment in S. cerevisiae. This region ofchromatin is an attractive target for validation studies as one cansupply yeast with galactose in place of glucose to rapidly andsynchronously stimulate transcriptional activation of GAL1—therebysetting a transcriptionally active chromatin state for epiproteomeanalysis. Cells were transformed with plasmids expressing a nucleaseinactive and PrA-tagged version of Cas9 (pPrA-Cas9) and/or expressinggRNA specific to the promoter region of the GAL1 gene (pgRNA-GAL1).Similar expression of PrA-Cas9 in glucose and galactose was demonstratedby Western-blotting (FIG. 10A). To evaluate whether expression of thisPrA-Cas9/gRNA complex affected transcription of GAL1, cDNA was preparedfrom cells in glucose (transcriptionally repressed GAL1) and galactose(transcriptionally active GAL1) and was analyzed by quantitativereal-time PCR. GAL1 transcription was similar in cells expressingPrA-Cas9/gRNA compared to cells expressing only PrA-Cas9, indicatingthat expression of PrA-Cas9/gRNA does not drastically altertranscriptional activation (FIG. 10B). To determine whether thisexpressed PrA-Cas9/gRNA complex was bound to and could enrich chromatinat the GAL1 promoter region, ChIP was performed to PrA-Cas9 in cellsfrom glucose and galactose cultures. GAL1 promoter chromatin wasenriched in a gRNA dependent manner with PrA-Cas9 from both glucose(4.9-fold) and galactose (70-fold) growth conditions (FIG. 10C). Regions2 kb up- or downstream did not show enrichment (FIG. 10C), demonstratingthat chromatin purification was localized to the gRNA target region. Inprevious studies using TAL proteins targeted to the same chromatinregion (Byrum et al., 2013), a ˜6-fold enrichment was observed undergalactose growth conditions and no enrichment under glucose growth.Therefore, the enrichment observed with PrA-Cas9/gRNA ingalactose-containing media is greater than an order of magnitude higherrelative to a TAL targeted to this region of chromatin.

To determine if enrichment using CRISPR-ChAP was specific, a series ofpotential off-target sites were analyzed (FIG. 10C). The four mostsimilar sites in the genome to the first 12 base-pairs of the 20base-pairs targeted at GAL1 by gRNA-GAL1 were analyzed by qPCR-ChIP forPrA-Cas9/gRNA binding. The first 12 base-pairs of the 20 base-pairtarget sequence strongly influence gRNA-directed binding specificity (Fuet al., 2013). The off-target (OT) sites contained 14/20 (OT1), 15/20(OT2), 15/20 (OT3) and 13/20 (OT4) of sequence identity relative to theGAL1 target DNA. Two of the four off-target sites showed 3.2- and4.4-fold (OT1 & OT2) enrichment with PrA-Cas9/gRNA (FIG. 10C). For mosteffective targeting of Cas9 to a genomic region, the 20 base-pair targetregion needs to contain a protospacer-activation motif (PAM motif)immediately 3′ to the target DNA. In the type II S. pyogenes system usedin this work, the PAM motif is NGG (Mali et al., 2013; DiCarlo et al.,2013). Accordingly, OT1 and OT2 that showed Cas9/gRNA enrichmentcontained a PAM motif, while OT3 and OT4 did not. This demonstrated thatoff-target binding of the PrA-Cas9/gRNA complex targeting GAL1 isenhanced with a PAM motif and can provide ˜4-fold off-target enrichment.This ˜4-fold off-target enrichment is much lower than the 70-foldenrichment observed for transcriptionally active GAL1 promoter chromatinand will not complicate large scale proteomic approaches as thespecifically bound proteins/PTMs will dominate the mass spectrometricdata collection. The enrichment of GAL1 promoter chromatin under glucosegrowth conditions was 4.9-fold whereas off-target binding can contributeup to ˜4-fold enrichments. Therefore, purification of GAL1 promoterchromatin under glucose growth conditions was not pursued for largescale proteomic analysis, but rather the 70-fold enriched chromatin fromgalactose growth conditions was used for subsequent proteomic studies.The Cas9/gRNA and previously reported TAL results illustrate thatDNA-binding affinity reagents may differentially access chromatin indifferent states; thus, care has to be taken to test for specificenrichment prior to proteomic studies (Byrum et al., 2013). As theCRISPR-based approaches become more engineered for DNA-bindingspecificity, off-target issues will have less impact on theCRISPR-ChAP-MS approach (Jiang et al., 2013).

To demonstrate the utility of the CRISPR-ChAP-MS approach, the GAL1promoter chromatin was enriched from 1×10¹⁰ cells that were grown inmedia containing galactose. As a control for quantitative massspectrometric identification of proteins as “specific” or “non-specific”to the purification, CRISPR-ChAP-MS was performed with PrA-Cas9expressing cells either with or without gRNA-GAL1. Of particularimportance for purification of small regions of chromatin, anexperimentally-determined amount of formaldehyde cross-linking andsonication must be used to ensure that a native chromatin region can beisolated and analyzed (Byrum et al., 2013; Byrum et al., 2012b; Byrum etal., 2011a). Cells were cross-linked with 1.25% formaldehyde, lysedunder cryogenic conditions with a ball mill, and after thawing weresonicated in purification buffer to yield chromatin fragments ˜1 kb inlength. Dynabeads coated with IgG were used to affinity purify thePrA-Cas9/gRNA complex or control PrA-Cas9 with any associated proteinsand posttranslationally modified histones. Isolated proteins wereresolved by SDS-PAGE (FIG. 11A), excised from the entire gel lane in 2mm bands and subjected to in-gel trypsin digestion. Tryptic peptideswere analyzed by high resolution mass spectrometry with a Thermo VelosOrbitrap mass spectrometer as reported (Byrum et al., 2013). Proteinsand histone PTMs (acetylation and mono-, di- and trimethylation oflysine) were identified with Mascot (Tables 9 & 10).

To determine which proteins were specifically enriched with the GAL1promoter chromatin, a quantitative mass spectrometric approach was usedto compare proteins identified with PrA-Cas9/gRNA and PrA-Cas9 alone.This reported approach uses normalized spectral abundance factors torepresent the relative level of each protein in each sample, which canthen be cross-compared to identify those proteins/PTMs enriched withPrA-Cas9/gRNA (Byrum et al., 2013; Zybailov et al., 2006; Byrum et al.,2013b). Using this approach, 86 out of 1832 identified proteins werefound to enrich with PrA-Cas9/gRNA (Table 9). 11 of the 86 proteins wererelated to transcription (Rebl, Spt5, Toa2, Bafl, Sin3, H2B2, Ume1,Pob3, Rsc6, Rpa14, Rsc7), while the other 75 were common contaminantsfound in affinity enrichments (Byrum et al., 2013; Byrum et al. 2012b).In addition to proteins, acetylation of lysine 14 on histone H3 (H3K14)and H3K23 were found enriched with the GAL1 promoter chromatin (Table10). Both H3K14ac and H3K23ac are correlated to active transcriptionalstates of chromatin. ChIP for a subset of these proteins/PTMs (Spt5,Pob3, Rsc6, Rsc7 and H3K14ac) was used to verify that theseproteins/PTMs are components of the epiproteome at the targeted regionof GAL1 promoter chromatin (FIG. 11B). H3K14ac was identified at theGAL1 promoter region with our first and second generation ChAPtechnologies (Byrum et al., 2013; Byrum et al. 2012b), while Pob3, Spt5,Rsc6 and Rsc7 are unique to this study. Pob3 forms a complex with Spt16to make yFACT, which promotes chromatin rearrangement to allowprogression of RNA polymerase. Spt16 was identified with our first andsecond generation ChAP technologies at GAL1 (Byrum et al., 2013; Byrumet al. 2012b); thus, providing compelling evidence that yFACT islocalized to this chromatin region during transcriptional activation.Spt5 is an elongation factor that aids RNA polymerase II, while the RSCcomplex of proteins serves as a chromatin remodeler that is involvedwith transcription. Taken together our results present a snapshot of thedynamics of transcriptional activation within a 1 kb viewing window atthe GAL1 promoter chromatin. This analysis demonstrates that theCRISPR-ChAP-MS approach can be used to identify a local epiproteome.

The CRISPR-ChAP-MS approach provides a new tool to study epigeneticregulation. Researchers can now identify proteins and histone PTMs at 1kb resolution using proteomic approaches that do not depend on a prioriknowledge of the protein/PTM target, which distinguishes this methodfrom traditional ChIP. Key to success with chromatin enrichmentprocedures is the quantitative mass spectrometry used to determine whichidentified proteins/PTMs are “specific” to the isolated chromatin. Thesemass spectrometric approaches can be label-free, as used here and in ourTAL-based second generation ChAP methodology (Byrum et al., 2013), orutilize an isotopically heavy label, as used in our LexA-based firstgeneration methodology (Byrum et al. 2012b). Relative to the TAL-basedand LexA-based ChAP methodology, our PrA-Cas9/gRNA approach showedgreatly enhanced enrichment of targeted chromatin, which is instrumentalfor analyzing low copy cellular entities like specific chromatinsections. Furthermore, the Cas9/gRNA system is easily manipulated bysimply altering the gRNA sequence, which provides for adaptability andmultiplexing approaches. Recent and future efforts to further engineerthe specificity of the Cas9/gRNA system will only expand thecapabilities of the CRISPR-ChAP-MS approach (Jiang et al., 2013). Thistechnology is immediately applicable to cell culture and in vivo systemsthat provide for expression of the Cas9/gRNA machinery. TheCRISPR-ChAP-MS approach suggests far-reaching applicability foridentifying molecular components driving chromosomal activities.

Methods for Example 6 Cloning, Western-Blotting, Real-Time ReverseTranscription PCR and Chromatin Immunoprecipitation (ChIP)

Cas9 was subcloned from Addgene plasmid 44246 (www.addgene.org/CRISPR/;Cross Lab) into pPrA-LexA (TRP1 selection) (Byrum et al. 2012b)—fusingCas9 with a PrA (Protein A) tag to make pPrA-Cas9. Addgene plasmid 43803(www.addgene.org/CRISPR/; Cross Lab) was used to express the gRNA (URA3selection). The gRNA sequence in the plasmid was mutated in two stepsusing a Stratagene site-directed mutagenesis kit to produce thefollowing sequence matching 20 base-pairs in the GAL1 promoter region:

(SEQ ID NO: 372) 5′ATTTGAAGGTTTGTGGGGCC.Three S. cerevisiae strains (W303 matA) were created by transforming theresulting plasmids: pgRNA-GAL1, pPrA-Cas9, and pPrA-Cas9+pgRNA-GAL1.Western-blotting, real-time reverse transcription PCR and chromatinimmunoprecipation (ChIP) were as described (Byrum et al. 2013; Byrum etal., 2012b). Off-target sites used in FIG. 10C were:

(SEQ ID NO: 373) OT1 5′ATGAAAAAATTAGTGGGGCC, (SEQ ID NO: 374)OT2 5′ATACGTAGTCTTGTGGGGCC, (SEQ ID NO: 375) OT3 5′TACGGAAGGTTGGTGGGGCC,(SEQ ID NO: 376) OT4 5′TATGTCGCGTTTGTGGGGCC.

CRISPR-ChAP-MS.

S. cerevisiae with pPrA-Cas9 or pPrA-Cas9+gRNA-GAL1 were grown tomid-log phase in synthetic yeast media (minus tryptophan and minustryptophan/uracil respectively) with 3% galactose and subjected to 1.25%formaldehyde cross-linking for 6 minutes. Cross-linking was quenchedwith 125 mM glycine for 5 minutes. Cells were collected bycentrifugation and lysed under cryogenic conditions (Byrum et al.,2012b). Lysate from 10¹⁰ cells was re-suspended in purification buffer(25 mM HEPES-KOH, 0.5 mM EGTA, 1 mM EDTA, 10% glycerol, 0.02% NP-40, 150mM KCl, 1× Sigma fungal protease inhibitor cocktail, 4 μg/mL PepstatinA, 2 mM PMSF) at 5 mL/gram cell lysate. Re-suspended cell lysate wassubjected to sonication with a Bioruptor to shear chromatin to ˜1 kb insize as described (Byrum et al. 2013; Byrum et al. 2012b). PrA-taggedCas9/gRNA complex and associated proteins were affinity purified on 144mg of IgG-coated Dynabeads (Byrum et al. 2013; Byrum et al. 2012b).IgG-coated beads were incubated with lysate for 7 hr at 4° C. withconstant agitation. Beads were collected with magnets and washed twicein purification buffer, once with purification buffer with 1 M NaCl/1 Murea, and once in purification buffer. Proteins were eluted from thewashed beads with 0.5 N ammonium hydroxide/0.5 mM EDTA for 5 minutes atroom temperature. Eluted proteins were lyophilized, re-suspended inLaemmli loading buffer, resolved by 4-20% gradient SDS-PAGE, andvisualized by colloidal Coomassie-staining. Gel lanes were sliced into 2mm sections and subjected to in-gel trypsin digestion (Byrum et al.2012b). Tryptic peptides were analyzed by high resolution tandem massspectrometry with a Thermo Velos Orbitrap mass spectrometer coupled to aWaters nanoACQUITY LC system (Byrum et al. 2013; Byrum et al. 2012b).Proteins and histone PTMs (lysine acetylation and methylation) wereidentified with Mascot (Tables 9 & 10). To determine if a protein was“specific” or “non-specific” to the purification, a previously reportedquantitative mass spectrometry approach was utilized (Byrum et al.2013). In brief, a normalized spectral abundance factor (NSAF) value wascalculated for each protein in the PrA-Cas9 and PrA-Cas9/gRNApurifications. The NSAF value is the number of spectral counts assignedto a given protein (normalized by the molecular weight of that protein)divided by the sum of all normalized spectral counts of all proteinsidentified in the specific purification (Zybailov et al., 2006). Afold-change of normalized NSAF values was then used to identify proteinsspecific to the PrA-Cas9/gRNA purification (Table 9).

References for Examples 1-6

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TABLE 1Proteins identified by Mascot Distiller from ChAP-MS analysis of GAL1 chromatinisolated from cells grown in glucose.Mascot Distiller Quantitation Report Mascot search results: GlucoseLog ratio versus Log ratio versus Intensity (all Intensity (selectedpositive ratios) ratios) L/ 0 1.00e+7 2.00e+7 0 5.00e+6 1.00e+7 (L +3.00e+7 4.00e+7 1.50e+7 2.00e+7 −4 −3 H) −15 −10 −5 0 5 −2 −1 0 1 HitAccession Score Mass L(L + H) SD(geo) # 1 P00925 1180 46885 0.5797 1.0097 ENO2_YEAST Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2 PE =1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ANLDVKDQK 0.8222 0.03008 0.050980.4849 14020.00 2 3 YDLDFKNPESDK 0.4886 0.04889 0.1516 0.7 2.59E+05 3 2YDLDFKNPESDK X 0.5785 0.01343 0.2062 0.9094 1.62E+05 4 2 AVDDFLLSLDGTANKX 0.5762 0.001 0.2292 0.9942 1.02E+07 5 3 AVDDFLLSLDGTANK X 0.57990.00158 0.6342 0.9975 8.26E+05 6 2 DGKYDLDFKNPESDK X 0.5622 0.008420.1735 0.989 1.71E+05 7 2 GVMNAVNNVNNVIAAAFVK 0.7536 0.05322 0.5940.4909 2.12E+05 8 3 YPIVSIEDPFAEDDWEAWSHF X 0.5768 0 0.8459 0.99952.58E+06 FK 9 3 RYPIVSIEDPFAEDDWEAWSH X 0.5641 0.0183 0.5271 0.97781.27E+05 FFK 10 3 YGASAGNVGDEGGVAPNIQTA X 0.5825 0 0.9229 0.99931.78E+07 EEALDLIVDAIK Hit Accession Score Mass L(L + H) SD(geo) # 2P00924 1117 46773 0.5798 1.008 5 ENO1_YEAST Enolase 1 OS =Saccharomyces cerevisiae GN = ENO1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ANIDVKDQK 0.8222 0.03008 0.05098 0.4849 1.40E+04 2 2 AVDDFLISLDGTANK X0.5762 0.001 0.2292 0.9942 1.02E+07 3 3 AVDDFLISLDGTANK X 0.5799 0.001580.6342 0.9975 8.26E+05 4 3 IEEELGDNAVFAGENFHHGDK X 0.6064 0.00518 0.50170.978 3.82E+05 L 5 3 YPIVSIEDPFAEDDWEAWSHF X 0.5768 0 0.8459 0.99952.58E+06 FK 6 3 RYPIVSIEDPFAEDDWEAWSH X 0.5641 0.0183 0.5271 0.97781.27E+05 FFK 7 3 YGASAGNVGDEGGVAPNIQTA X 0.5825 0 0.9229 0.9993 1.78E+07EEALDLIVDAIK Hit Accession Score Mass L(L + H) SD(geo) # 3 P10592 56569844 0.5495 10 H5P72_YEAST Heat shock protein SSA2 OS =Saccharomyces cerevisiae GN = SSA2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ITITNDKGR X 0.9873 0.0152 0.06237 0.9611 4.21E+04 2 2 NFNDPEVQGDMK X0.554 0.0076 0.3809 0.9603 8.52E+05 3 2 FKEEDEKESQR X 0.5702 0.00880.0696 0.9865 9.27E+04 4 2 NFTPEQISSMVLGK X 0.5605 0.00872 0.1288 0.95085.66E+05 5 2 LIDVDGKPQIQVEFK X 0.5488 0.00255 0.256 0.9909 4.00E+05 6 3LIDVDGKPQIQVEFK X 0.5555 0.00158 0.624 0.9945 2.37E+06 7 3IINEPTAAAIAYGLDKK X 0.5399 0.00584 0.05784 0.938 3.22E+05 8 3LDKSQVDEIVLVGGSTR X 0.528 0.02077 0.3666 0.7616 7.53E+05 9 3NTISEAGDKLEQADKDAVTK X 0.5444 0.00255 0.3405 0.9868 2.60E+06 10 3TQDLLLLDVAPLSLGIETAGGV X 0.5041 0.07248 0.196 0.9741 1.75E+05 MTK HitAccession Score Mass L(L + H) SD(geo) # 4 P06169 555 61737 0.5581 1.0085 PDC1_YEAST Pyruvate decarboxylase isozyme 1 OS =Saccharomyces cerevisiae GN = PDC1 PE = 1 SV = 7 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NATFPGVQMK X 0.5499 0.00466 0.3978 0.9842 1.13E+06 2 3 VATTGEWDKLTQDK X0.5476 0.00455 0.265 0.9899 1.17E+06 3 3 LLQTPIDMSLKPNDAESEK X 0.56350.00264 0.4617 0.9956 2.39E+05 4 2 MIEIMLPVFDAPQNLVEQAK X 0.5603 0.00380.7877 0.9907 7.07E+06 5 3 LLQTPIDMSLKPNDAESEKEVI X 0.56 0.00158 0.56860.9967 2.71E+06 DTILALVK Hit Accession Score Mass L(L + H) SD(geo) # 5P10591 551 70039 0.5549 9 H5P71_YEAST Heat shock protein SSA1 OS =Saccharomyces cerevisiae GN = SSA1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ITITNDKGR X 0.9873 0.0152 0.06237 0.9611 4.21E+04 2 2 NFNDPEVQADMK X0.595 0.00755 0.1662 0.9451 4.27E+05 3 2 FKEEDEKESQR X 0.5702 0.00880.0696 0.9865 9.27E+04 4 2 NFTPEQISSMVLGK X 0.5605 0.00872 0.1288 0.95085.66E+05 5 2 LIDVDGKPQIQVEFK X 0.5488 0.00255 0.256 0.9909 4.00E+05 6 3LIDVDGKPQIQVEFK X 0.5555 0.00158 0.624 0.9945 2.37E+06 7 3IINEPTAAAIAYGLDKK X 0.5399 0.00584 0.05784 0.938 3.22E+05 8 3LDKSQVDEIVLVGGSTR X 0.528 0.02077 0.3666 0.7616 7.53E+05 9 3TQDLLLLDVAPLSLGIETAGGV X 0.5041 0.07248 0.196 0.9741 1.75E+05 MTK HitAccession Score Mass L(L + H) SD(geo) # 6 P15108 548 80850 0.4277 10HSC82_YEAST ATP-dependent molecular chaperone HSC82 OS =Saccharomyces cerevisiae GN = H5C82 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SPFLDALK X 0.594 0.00899 0.5359 0.9605 4.97E+05 2 3 ALKDILGDQVEK X0.5513 0.02217 0.189 0.9214 5.90E+04 3 3 VKEEVQELEELNK X 0.5794 0.010430.07342 0.9201 7.47E+04 4 2 LEEVDEEEEEKKPK 0.1049 999 0.1111 0.16432.69E+04 5 2 LFLKDDQLEYLEEK X 0.5684 0.02513 0.191 0.9399 5.88E+05 6 3LFLKDDQLEYLEEKR X 0.4997 0.04689 0.1356 0.8192 3.36E+05 7 3TLVDITKDFELEETDEEK X 0.4212 0.04847 0.09843 0.7318 2.17E+05 8 2VFITDEAEDLIPEWLSFVK X 0.5569 0.00991 0.227 0.9585 1.35E+06 9 3VFITDEAEDLIPEWLSFVK X 0.5764 0.00772 0.5192 0.9965 3.80E+05 10 3RVFITDEAEDLIPEWLSFVK X 0.5766 0.02142 0.2893 0.9293 1.19E+05 11 3TLVDITKDFELEETDEEKAER X 0.216 0.1336 0.2606 0.801 1.35E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 7 P00560 506 44711 0.5584 4PGK_YEAST Phosphoglycerate kinase OS = Saccharomyces cerevisiae GN =PGK1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 VDFNVPLDGKK X 0.3003 0.01134 0.10590.8842 3.08E+05 2 2 VLENTEIGDSIFDK 0.9928 0.00158 0.8106 0.3129 3.18E+073 2 SSAAGNTVIIGGGDTATVAK X 0.577 0.00158 0.6503 0.9976 1.77E+06 4 3GVEVVLPVDFIIADAFSADANT X 0.6021 0.00634 0.4734 0.9828 1.32E+06 K 5 2GVEVVLPVDFIIADAFSADANT X 0.5722 0.00525 0.5529 0.9973 1.42E+06 K HitAccession Score Mass L(L + H) SD(geo) # 8 P00359 492 35724 0.5592 1.0175 G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase 3 OS =Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ELDTAQK X 0.5482 0.00832 0.1767 0.9264 2.25E+04 2 2 VVDLVEHVAK X 0.55570.001 0.6963 0.9976 2.33E+06 3 2 YAGEVSHDDK 0.7269 0.01789 0.2422 0.69888.10E+04 4 2 TASGNIIPSSTGAAK X 0.5621 0.00158 0.7985 0.9966 9.13E+06 5 3VPTVDVSVVDLTVK X 0.5299 0.00836 0.3828 0.9782 2.33E+05 6 3YAGEVSHDDKHIIVDGK 0.4138 0.03022 0.1569 0.4338 1.27E+06 7 2YAGEVSHDDKHIIVDGK 0.4604 0.01421 0.386 0.4585 4.81E+05 8 2DPANLPWGSSNVDIAIDSTGV X 0.5497 0.00466 0.5417 0.9953 1.10E+06 FK HitAccession Score Mass L(L + H) SD(geo) # 9 P00950 289 27592 0.5753 1.0284 PMG1_YEAST Phosphoglycerate mutase 1 OS =Saccharomyces cerevisiae GN = GPM1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3KVYPDVLYTSK X 0.6133 0.00839 0.05839 0.9039 9.79E+04 2 2 LLPYWQDVIAK X0.5686 0.001 0.6124 0.9984 3.23E+06 3 2 SFDVPPPPIDASSPFSQK X 0.5790.00467 0.7461 0.9747 5.95E+06 4 3 RSFDVPPPPIDASSPFSQK X 0.5607 0.00550.1214 0.9811 2.74E+05 Hit Accession Score Mass L(L + H) SD(geo) # 10P00942 273 26779 0.8938 1.241 4TPIS_YEAST Triosephosphate isomerase OS = Saccharomyces cerevisiae GN =TPI1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 KPQVTVGAQNAYLK X 1 0 0.6505 0.74072.01E+06 2 2 ASGAFTGENSVDQIK X 0.8721 0.00784 0.8579 0.9988 1.90E+06 3 3SYFHEDDKFIADK X 0.5635 0.00564 0.2565 0.9791 2.28E+05 4 2ASGAFTGENSVDQIKDVGAK X 0.5037 0.05902 0.5738 0.8696 1.28E+05 HitAccession Score Mass L(L + H) SD(geo) # 11 P23254 258 74104 0.5924 1.0894 TKT1_YEAST Transketolase 1 OS = Saccharomyces cerevisiae GN =TKL1 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LFSEYQK 0.7783 0.02398 0.136 0.64681.69E+05 2 2 ILAVDTVSK X 0.6661 0.02039 0.1191 0.8514 6.18E+05 3 3KFPELGAELAR X 0.4889 0.01828 0.08146 0.9458 3.41E+04 4 2 LSGQLPANWESK0.9991 0.00158 0.5921 0.6509 1.69E+06 5 2 VVSLPDFFTFDK X 0.5277 0.017460.3974 0.82 4.93E+05 6 2 QNLPQLEGSSIESASK X 0.5395 0.00842 0.1282 0.97679.63E+04 7 2 SFVVPQEVYDHYQK 0.4152 0.04681 0.3912 0.41 1.50E+05 HitAccession Score Mass L(L + H) SD(geo) # 12 P34760 251 21688 0.5583 1TSA1_YEAST Peroxiredoxin TSAI OS = Saccharomyces cerevisiae GN =TSA1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 TAVVDGVFDEVSLDK X 0.5583 0.013410.4102 0.9415 7.29E+05 Hit Accession Score Mass L(L + H) SD(geo) # 13P02994 242 50001 0.5996 5 EF1A_YEAST Elongation factor 1-alpha OS =Saccharomyces cerevisiae GN = TEF1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H Std. Err. Fraction Correlation Intensity cations 1 2FQEIVK X 0.9909 0.00329 0.1232 0.9948 5.97E+05 2 2 LPLQDVYK X 0.52660.002 0.5985 0.9845 4.55E+06 3 3 SHINVVVIGHVDSGK X 0.5427 0.010930.07069 0.9813 4.33E+04 4 3 TLLEAIDAIEQPSRPTDKPLR X 0.6222 0.01 0.38090.7963 1.58E+07 5 3 SVEMHHEQLEQGVPGDNVGF X 0.5271 0.00255 0.8205 0.99722.24E+06 NVK Hit Accession Score Mass L(L + H) SD(geo) # 14 P11484 23566937 0.5697 1.042 3 HSP75_YEAST Heat shock protein SSB1 OS =Saccharomyces cerevisiae GN = SSB1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LLSDFFDGK X 0.5313 0.004 0.3939 0.9936 1.18E+06 2 2 VIDVDGNPVIEVQYLEETKX 0.5573 0.03139 0.2885 0.9312 2.81E+05 3 3 STSGNTHLGGQDFDTNLLEHF X0.6018 0.01912 0.5754 0.975 1.64E+06 K Hit Accession Score Mass L(L + H)SD(geo) # 15 P16521 220 115920 0.4751 1.086 3EF3A_YEAST Elongation factor 3A OS = Saccharomyces cerevisiae GN =YEF3 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 QINENDAEAMNK X 0.502 0.03789 0.19310.9204 1.87E+05 2 2 ATETVDNKDIER X 0.5572 0.01016 0.3336 0.9535 2.92E+053 2 LVEDPQVIAPFLGK X 0.4314 0.01731 0.1193 0.9722 5.89E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 16 P14540 217 39812 0.5455 1.017 4ALF_YEAST Fructose-bisphosphate aldolase OS =Saccharomyces cerevisiae GN = FBA1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LLPWFDGMLEADEAYFK X 0.5387 0.01791 0.6343 0.9901 2.73E+06 2 3LLPWFDGMLEADEAYFK X 0.5693 0.00324 0.7442 0.9942 4.58E+05 3 2KLLPWFDGMLEADEAYFK X 0.5497 0.02627 0.3049 0.8469 4.81E+04 4 3KLLPWFDGMLEADEAYFK X 0.5579 0.00588 0.6699 0.9919 6.41E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 17 P05750 214 26630 0.5144 1RS3_YEAST 40S ribosomal protein S3 OS = Saccharomyces cerevisiae GN =RPS3 PE = 1 SV = 5 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 ALPDAVTIIEPKEEEPILAPSVK X 0.51440.00787 0.0782 0.9853 1.22E+06 Hit Accession Score Mass L(L + H) SD(geo)# 18 P38788 196 58515 0.5268 1.003 2SSZ1_YEAST Ribosome-associated complex subunit SSZ1 OS =Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EAVLTVPTNFSEEQK X 0.5251 0.00574 0.2728 0.9966 3.66E+05 2 3LISDYDADELAEALQPVIVNTP X 0.5276 0.00557 0.6012 0.9986 7.77E+05 HLK HitAccession Score Mass L(L + H) SD(geo) # 19 P40150 195 66930 0.5697 1.0423 HSP76_YEAST Heat shock protein SSB2 OS = Saccharomyces cerevisiae GN =SSB2 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LLSDFFDGK X 0.5313 0.004 0.3939 0.99361.18E+06 2 2 VIDVDGNPVIEVQYLEETK X 0.5573 0.03139 0.2885 0.9312 2.81E+053 3 STSGNTHLGGQDFDTNLLEHF X 0.6018 0.01912 0.5754 0.975 1.64E+06 K HitAccession Score Mass L(L + H) SD(geo) # 20 P32324 189 93719 0.4948 1.1414 EF2_YEAST Elongation factor 2 OS = Saccharomyces cerevisiae GN =EFT1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 TGTLTTSETAHNMK X 0.5494 0.05488 0.25740.9685 3.09E+04 2 2 ETVESESSQTALSK X 0.4964 0.00945 0.5999 0.9891.00E+06 3 3 WTNKDTDAEGKPLER X 0.4881 0.01896 0.04008 0.9109 1.19E+05 42 WTNKDTDAEGKPLER X 0.383 0.06499 0.03736 0.93 1.87E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 21 P32589 184 77318 0HSP7F_YEAST Heat shock protein homolog SSE1 OS =Saccharomyces cerevisiae GN = SSE1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3QVEDEDHMEVFPAGSSFPSTK 0.6809 0.02791 0.3031 0.3098 9.21E+05 2 3QSISEAFGKPLSTTLNQDEAIA 0.5365 0.06281 0.4112 0.2745 3.29E+05 K HitAccession Score Mass L(L + H) SD(geo) # 22 P54115 183 54380 0.6157 1ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase, cytosolic OS =Saccharomyces cerevisiae GN = ALD6 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SAHLVFDDANIKK X 0.6157 0.0168 0.06354 0.9683 1.83E+04 2 3IVKEEIFGPVVTVAK 0.01367 0.6603 0.692 0.03687 2.37E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 23 P00360 179 35728 0.5624 1.059 4G3P1_YEAST Glyceraldehyde-3-phosphate dehydrogenase 1 OS =Saccharomyces cerevisiae GN = TDH1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ELDTAQK X 0.5482 0.00832 0.1767 0.9264 2.25E+04 2 2 TASGNIIPSSTGAAK X0.5621 0.00158 0.7985 0.9966 9.13E+06 3 3 VPTVDVSVVDLTVK X 0.52990.00836 0.3828 0.9782 2.33E+05 4 3 IATYQERDPANLPWGSLK X 0.6109 0.008940.4762 0.9875 2.36E+05 Hit Accession Score Mass L(L + H) SD(geo) # 24P05694 159 86296 0.5474 1.143 4METE_YEAST 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferaseOS = Saccharomyces cerevisiae GN = MET6 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VATSGVANK X 0.4292 0.05981 0.2367 0.7626 5.78E+05 2 2 ITVDELFK X 0.76130.02167 0.4122 0.9349 3.00E+05 3 2 ALDADVVSIEFSK X 0.5995 0.00506 0.36170.9908 4.15E+05 4 3 APEQFDEVVAAIGNK X 0.5769 0.02178 0.2145 0.92287.39E+04 Hit Accession Score Mass L(L + H) SD(geo) # 25 P00817 159 322800.3148 1.707 2 IPYR_YEAST Inorganic pyrophosphatase OS =Saccharomyces cerevisiae GN = IPP1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LNDIEDVEK X 0.1915 0.08967 0.192 0.967 2.15E+05 2 3 LEITKEETLNPIIQDTKK0.5691 0.01513 0.1321 0.6614 3.55E+04 3 3 AVGDNDPIDVLEIGETIAYTGQ X0.5565 0.00915 0.5386 0.9951 1.89E+05 VK Hit Accession Score Mass L(L +H) SD(geo) # 26 P46655 156 81369 0.4215 1.269 2SYEC_YEAST Glutamyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KNDDGSMVAK X 0.5902 0.05607 0.0228 0.8152 515.7 2 3 EKEEFQDSILEDLDLLGIKX 0.4214 0.04183 0.2818 0.7588 6.23E+05 Hit Accession Score Mass L(L +H) SD(geo) # 27 P09436 156 123651 0.9973 1SYIC_YEAST Isoleucyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = ILS1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2MSNIDFQYDDSVK X 0.9973 0.00158 0.6248 0.961 3.01E+06 Hit Accession ScoreMass L(L + H) SD(geo) # 28 P61864 148 8552 0.8538 1UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN = UBI1 PE = 1 SV =1 Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 IQDKEGIPPDQQR X 0.8538 0.01276 0.1534 0.87561.67E+05 Hit Accession Score Mass L(L + H) SD(geo) # 29 P04456 146 157480.5126 1 RL25_YEAST 60S ribosomal protein L25 OS =Saccharomyces cerevisiae GN = RPL25 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ELYEVDVLK X 0.5126 0.00785 0.1734 0.9804 4.97E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 30 P12709 146 61261 0.5947 3G6PI_YEAST Glucose-6-phosphate isomerase OS =Saccharomyces cerevisiae GN = PGI1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NWFLSK X 0.5893 0.01445 0.08506 0.8965 1.22E+04 2 2 TFTTAETITNANTAK0.7863 0.02669 0.2797 0.4859 1.42E+05 3 2 NLVNDEIIAALIELAK X 0.74450.01763 0.05341 0.9308 1.58E+04 4 3 ANKPMYVDGVNVAPEVDSVLK X 0.58980.03119 0.315 0.7014 4.18E+05 Hit Accession Score Mass L(L + H) SD(geo)# 31 P08524 145 40738 0.5181 1FPPS_YEAST Farnesyl pyrophosphate synthase OS =Saccharomyces cerevisiae GN = FPP1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TVEQLGQEEYEK X 0.5181 0.00585 0.1843 0.9906 4.80E+05 2 2 IEQLYHEYEESIAK0.3587 0.08308 0.1586 0.6297 6.38E+04 Hit Accession Score Mass L(L + H)SD(geo) # 32 P00330 142 36800 0.5295 1.039 3ADH1_YEAST Alcohol dehydrogenase 1 OS = Saccharomyces cerevisiae GN =ADH1 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ANELLINVK X 0.5781 0.01445 0.4060.9865 4.01E+05 2 2 VVGLSTLPEIYEK X 0.518 0.001 0.6074 0.9963 5.17E+06 33 VLGIDGGEGKEELFR X 0.5414 0.00403 0.7131 0.9802 3.52E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 33 P07262 138 49763 0.2171 1DHE4_YEAST NADP-specific glutamate dehydrogenase 1 OS =Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3VTWENDKGEQEVAQGYR X 0.2171 0.1184 0.5086 0.7666 6.81E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 34 P31373 138 42692 0.6023 1.05 2CYS3_YEAST Cystathionine gamma-lyase OS = Saccharomyces cerevisiae GN =CYS3 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ISVGIEDTDDLLEDIK X 0.613 0.008870.1862 0.967 6.82E+05 2 3 ISVGIEDTDDLLEDIKQALK X 0.5634 0.01345 0.34810.9112 1.80E+05 Hit Accession Score Mass L(L + H) SD(geo) # 35 P22202137 70009 0.5832 1.457 2 HSP74_YEAST Heat shock protein SSA4 OS =Saccharomyces cerevisiae GN = SSA4 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ITITNDKGR X 0.9873 0.0152 0.06237 0.9611 4.21E+04 2 3 IINEPTAAAIAYGLDKKX 0.5399 0.00584 0.05784 0.938 3.22E+05 Hit Accession Score Mass L(L +H) SD(geo) # 36 A6ZP47 134 65697 0.3172 1DED1_YEAS7 ATP-dependent RNA helicase DED1 OS =Saccharomyces cerevisiae (strain YJM789) GN = DED1 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations 1 2 TGGFLFPVLSESFK X 0.3172 0.03297 0.08265 0.8019 3.08E+05 2 3DVPEPITEFTSPPLDGLLLENIK 0.00052 7.122 0.6671 0.1659 1.16E+06 HitAccession Score Mass L(L + H) SD(geo) # 37 P00549 134 54510 0.5402 2.3752 KPYK1_YEAST Pyruvate kinase 1 OS = Saccharomyces cerevisiae GN =PYK1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 EVLGEQGKDVK 0.8211 0.01418 0.55870.4163 9.19E+05 2 3 MNFSHGSYEYHK X 0.159 0.3656 0.233 0.8491 3.57E+04 33 GVNLPGTDVDLPALSEKDKED X 0.5499 0.00705 0.3217 0.9634 2.45E+06 LR HitAccession Score Mass L(L + H) SD(geo) # 38 P29311 134 30073 0.5686 1.0633 BMH1_YEAST Protein BMH1 OS = Saccharomyces cerevisiae GN = BMH1 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 LAEQAERYEEMVENMK X 0.6493 0.019230.1302 0.8619 2.33E+04 2 3 QAFDDAIAELDTLSEESYK X 0.5798 0.00382 0.38750.9933 2.42E+05 3 3 ISDDILSVLDSHLIPSATTGESK X 0.5643 0.01199 0.12890.8075 1.04E+06 Hit Accession Score Mass L(L + H) SD(geo) # 39 P26321133 33890 0 RL5_YEAST 60S ribosomal protein L5 OS =Saccharomyces cerevisiae GN = RPL5 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 40 P26263 130 61542 0PDC6_YEAST Pyruvate decarboxylase isozyme 3 OS =Saccharomyces cerevisiae GN = PDC6 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 41 A6ZQJ1 121 44837 0.5295 1IF4A_YEAS7 ATP-dependent RNA helicase elF4A OS =Saccharomyces cerevisiae (strain YJM789) GN = TIF1 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations 1 3 AIMPIIEGHDVLAQAQSGTGK X 0.5295 0.00498 0.5721 0.98454.30E+05 Hit Accession Score Mass L(L + H) SD(geo) # 42 Q02753 119 182310.4842 1 RL21A_YEAST 60S ribosomal protein L21-A OS =Saccharomyces cerevisiae GN = RPL21A PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VGDIVDIK X 0.4842 0.00614 0.01566 0.9582 1.27E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 43 P05030 119 99941 0.5928 1PMA1_YEAST Plasma membrane ATPase 1 OS = Saccharomyces cerevisiae GN =PMA1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 TVEEDHPIPEDVHENYENK X 0.5928 0.022450.3764 0.8651 3.27E+05 Hit Accession Score Mass L(L + H) SD(geo) # 44Q03195 119 68297 0 RLI1_YEAST Translation initiation factor RLI1 OS =Saccharomyces cerevisiae GN = RLI1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LLAGALKPDEGQDIPK 0.1154 0.2281 0.1563 0.679 1.09E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 45 P38011 119 34936 0.4788 1GBLP_YEAST Guanine nucleotide-binding protein subunit beta-like protein OS =Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3VVPNEKADDDSVTIISAGNDK X 0.4788 0.00934 0.03497 0.9434 2.43E+05 HitAccession Score Mass L(L + H) SD(geo) # 46 P19097 117 206818 0.6972 1FAS2_YEAST Fatty acid synthase subunit alpha OS =Saccharomyces cerevisiae GN = FAS2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EIYYTPDPSELAAK X 0.6972 0.02896 0.2436 0.8764 4.39E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 47 P22768 116 47175 0ASSY_YEAST Argininosuccinate synthase OS = Saccharomyces cerevisiae GN =ARG1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 48 P41277 112 28138 0.5193 1.003 2GPP1_YEAST (DL)-glycerol-3-phosphatase 1 OS =Saccharomyces cerevisiae GN = GPP1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FAPDFADEEYVNK 0.2622 0.08634 0.2384 0.6536 3.56E+05 2 3FAPDFADEEYVNKLEGEIPEK X 0.5189 0.00547 0.2526 0.9631 1.44E+06 3 2VGEYNAETDEVELIFDDYLYAK X 0.5217 0.01439 0.5462 0.9935 2.38E+05 HitAccession Score Mass L(L + H) SD(geo) # 49 P49090 110 64857 0.5527 1.0532 ASNS2_YEAST Asparagine synthetase [glutamine-hydrolyzing] 2 OS =Saccharomyces cerevisiae GN = ASN2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YFTPDWLDEK X 0.5819 0.02038 0.1065 0.9343 3.09E+05 2 3AFDTTDEPDVKPYLPEEILWR X 0.5251 0.03417 0.2562 0.9393 3.11E+05 HitAccession Score Mass L(L + H) SD(geo) # 50 P15624 110 67691 0.9837 1.0763 SYFB_YEAST Phenylalanyl-tRNA synthetase beta chain OS =Saccharomyces cerevisiae GN = FRS1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SKEGAEPK X 0.9916 0.00141 0.07152 0.9856 1.79E+06 2 2 GYWIEEDDSVK X0.8641 0.05554 0.05094 0.8192 3.24E+04 3 2 NSGFEIIQGLLGK X 0.87040.03036 0.142 0.8105 8.54E+04 Hit Accession Score Mass L(L + H) SD(geo)# 51 P19882 109 60714 0.4595 1HSP60_YEAST Heat shock protein 60, mitochondrial OS =Saccharomyces cerevisiae GN = HSP60 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NVLIEQPFGPPK 0.3833 0.07553 0.1289 0.6499 8.66E+04 2 2 AAVEEGILPGGGTALVKX 0.4595 0.03115 0.1117 0.9559 1.38E+05 Hit Accession Score Mass L(L +H) SD(geo) # 52 P38088 109 75845 0SYG_YEAST Glycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae GN =GRS1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 53 P07284 105 53276 0SYSC_YEAST Seryl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = SES1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 54 P53184 99 24978 0.4323 1PNC1_YEAST Nicotinamidase OS = Saccharomyces cerevisiae GN = PNC1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 TTVLLDYTRPISDDPEVINK X 0.4323 0.025390.2814 0.7218 1.46E+06 Hit Accession Score Mass L(L + H) SD(geo) # 55P36008 99 46827 0.8918 1.457 2EF1G2_YEAST Elongation factor 1-gamma 2 OS =Saccharomyces cerevisiae GN = TEF4 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LLGSDVIEK X 0.9663 0.00996 0.4982 0.9961 1.44E+06 2 2 WFNTVAASPIVK X0.527 0.01203 0.07669 0.8876 2.21E+05 Hit Accession Score Mass L(L + H)SD(geo) # 56 Q01560 95 45444 0 NOP3_YEAST Nucleolar protein 3 OS =Saccharomyces cerevisiae GN = NPL3 PE =  SV = 1 Modifi- z Sequence Incl.L(L + H) Std. Err. Fraction Correlation Intensity cations Hit AccessionScore Mass L(L + H) SD(geo) # 57 P40213 94 15974 0RS16_YEAST 40S ribosomal protein S16 OS = Saccharomyces cerevisiae GN =RPS16A PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 2 YVDEQSKNELK 0.9917 0.004340.3579 0.08027 4.77E+05 2 2 YVDEQSKNELKK 0.9999 0.00574 0.1204 0.11644.58E+05 Hit Accession Score Mass L(L + H) SD(geo) # 58 P16140 94 579220 VATB_YEAST V-type proton ATPase subunit B OS =Saccharomyces cerevisiae GN = VMA2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 59 P25293 93 47855 0.5024 1NAP1_YEAST Nucleosome assembly protein OS =Saccharomyces cerevisiae GN = NAP1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LGSLVGQDSGYVGGLPK X 0.5024 0.03188 0.08129 0.758 2.53E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 60 P41940 93 39781 0.5624 1.009 2MPG1_YEAST Mannose-1-phosphate guanyltransferase OS =Saccharomyces cerevisiae GN = MPG1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LATGANIVGNALIDPTAK X 0.5695 0.00687 0.05507 0.9887 2.54E+04 2 3INAGLYILNPEVIDLIEMKPTSIE X 0.562 0.00414 0.5133 0.9966 4.50E+05 K HitAccession Score Mass L(L + H) SD(geo) # 61 P15705 93 66705 0STI1_YEAST Heat shock protein STI1 OS = Saccharomyces cerevisiae GN =STI1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 62 Q03048 91 15979 0 COFI_YEAST Cofilin OS =Saccharomyces cerevisiae GN = COF1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SGVAVADESLTAFNDLK 0.2984 0.1196 0.0948 0.4874 1.00E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 63 P38707 90 62168 0.6442 1SYNC_YEAST Asparaginyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = DED81 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SVQYVLEDPIAGPLVK X 0.6442 0.02511 0.182 0.8768 2.97E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 64 P49089 89 64734 0.4454 1.252 2ASNS1_YEAST Asparagine synthetase [glutamine-hydrolyzing] 1 OS =Saccharomyces cerevisiae GN = ASN1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YFTPDWLDEK X 0.5819 0.02038 0.1065 0.9343 3.09E+05 2 2 ATNDVEPSTYDSK X0.375 0.01032 0.3126 0.9726 4.80E+05 Hit Accession Score Mass L(L + H)SD(geo) # 65 P14832 88 17380 0CYPH_YEAST Peptidyl-prolyl cis-trans isomerase OS =Saccharomyces cerevisiae GN = CPR1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KVESLGSPSGATK 0.5598 0.00415 0.2553 0.5249 4.83E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 66 P0C0W9 86 19844 0.3135 1RL11A_YEAST 60S ribosomal protein L11-A OS =Saccharomyces cerevisiae GN = RPL11A PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VLEQLSGQTPVQSK 0.000776 0.4364 0.8707 0.2733 1.50E+07 2 3 VLEQLSGQTPVQSKX 0.3135 0.169 0.1611 0.8233 1.39E+04 Hit Accession Score Mass L(L + H)SD(geo) # 67 P14120 84 11504 0.5841 1RL30_YEAST 60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN =RPL30 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 VYYFQGGNNELGTAVGK X 0.5841 0.025820.205 0.8988 9.20E+04 Hit Accession Score Mass L(L + H) SD(geo) # 68P26755 84 13863 0 RFA3_YEAST Replication factor A protein 3 OS =Saccharomyces cerevisiae GN = RFA3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 69 P04147 83 64304 0PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear OS =Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TAEQLENLNIQDDQK 0.001099 1.859 0.4682 0.9671 3.84E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 70 P32527 82 49439 0ZUO1_YEAST Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations Hit Accession Score Mass L(L + H) SD(geo) # 71 P3862582 58750 0.5454 1 GUAA_YEAST GMP synthase [glutamine-hydrolyzing] OS =Saccharomyces cerevisiae GN = GUA1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VTYDITSKPPATVEWE X 0.5454 0.01078 0.239 0.9456 3.32E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 72 P31412 80 44434 0.6452 1VATC_YEAST V-type proton ATPase subunit C OS =Saccharomyces cerevisiae GN = VMA5 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IGSLDTLIVESEELSK X 0.6452 0.01519 0.07177 0.9753 2.77E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 73 P05753 80 29608 0RS4_YEAST 40S ribosomal protein S4 OS = Saccharomyces cerevisiae GN =RPS4A PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 74 P26783 79 25023 0.4952 1 RS5_YEAST 40S ribosomal protein S5 OS =Saccharomyces cerevisiae GN = RPS5 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3TIAETLAEELINAAK X 0.4952 0.0071 0.5691 0.9574 1.53E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 75 P17076 76 28396 0RL8A_YEAST 60S ribosomal protein L8-A OS = Saccharomyces cerevisiae GN =RPL8A PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 76 P53030 76 24470 0.5139 1 RL1_YEAST 60S ribosomal protein L1 OS =Saccharomyces cerevisiae GN = RPL1A PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FPTPVSHNDDLYGK X 0.5139 0.02598 0.07442 0.8939 3.55E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 77 P25694 74 92331 0.5765 1CDC48_YEAST Cell division control protein 48 OS =Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2AAAPTVVFLDELDSIAK X 0.5765 0.01988 0.2107 0.9888 1.27E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 78 P40303 73 28574 0PSA7_YEAST Proteasome component PRE6 OS = Saccharomyces cerevisiae GN =PRE6 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 79 P16861 73 108408 0K6PF1_YEAST 6-phosphofructokinase subunit alpha OS =Saccharomyces cerevisiae GN = PFK1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 80 P35691 73 18729 0TCTP_YEAST Translationally-controlled tumor protein homolog OS =Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LQETNPEEVPKFEK 0.01574 0.05686 0.3046 0.3037 2.21E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 81 P05738 72 21556 0.6443 1RL9A_YEAST 60S ribosomal protein L9-A OS = Saccharomyces cerevisiae GN =RPL9A PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 FLDGIYVSHK X 0.6443 0.01495 0.19130.8882 2.99E+04 2 3 YIQTEQQIEVPEGVTVSIK 0.008727 0.6329 0.355 0.43971.88E+06 Hit Accession Score Mass L(L + H) SD(geo) # 82 P00899 71 567320 TRPE_YEAST Anthranilate synthase component 1 OS =Saccharomyces cerevisiae GN = TRP2 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 83 P17079 71 17956 0.5847 1RL12_YEAST 60S ribosomal protein L12 OS = Saccharomyces cerevisiae GN =RPL12A PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 3 VDFKNPHDIIEGINAGEIEIPEN X0.5847 0.02535 0.1429 0.8697 3.12E+05 Hit Accession Score Mass L(L + H)SD(geo) # 84 P07806 70 126596 0.4001 1.235 2SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS =Saccharomyces cerevisiae GN = VAS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TGVFEPEFTADGK X 0.365 0.03845 0.2789 0.8561 4.52E+05 2 2 LNTAISNLEVENK X0.5312 0.02003 0.0767 0.9905 1.46E+05 Hit Accession Score Mass L(L + H)SD(geo) # 85 P26781 70 17898 0.4992 1RS11_YEAST 40S ribosomal protein S11 OS = Saccharomyces cerevisiae GN =RPS11A PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 2 TAIEGSYIDKK X 0.4992 0.00410.1365 0.9905 1.73E+05 Hit Accession Score Mass L(L + H) SD(geo) # 86P53252 70 38326 0.5822 1PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1 OS =Saccharomyces cerevisiae GN = PIL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2APTASQLQNPPPPPSTTK X 0.5822 0.02737 0.2412 0.8526 1.83E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 87 P22943 68 11686 0HSP12_YEAST 12 kDa heat shock protein OS = Saccharomyces cerevisiae GN =HSP12 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 GKDNAEGQGESLADQAR 0.01324 0.72910.2434 0.4791 3.47E+04 Hit Accession Score Mass L(L + H) SD(geo) # 88P02407 67 15891 0 RS17A_YEAST 40S ribosomal protein S17-A OS =Saccharomyces cerevisiae GN = RPS17A PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 89 P04801 66 84467 0SYTC_YEAST Threonyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TVSQADFPGLEGVAK 0.9625 0.01322 0.639 0.3281 3.05E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 90 P09733 63 49945 0TBA1_YEAST Tubulin alpha-1 chain OS = Saccharomyces cerevisiae GN =TUB1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 91 P33204 62 19959 0ARPC4_YEAST Actin-related protein 2/3 complex subunit 4 OS =Saccharomyces cerevisiae GN = ARC19 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 92 P23301 62 17208 0.4447 1IF5A2_YEAST Eukaryotic translation initiation factor 5A-2 OS =Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3KLEDLSPSTHNMEVPVVK X 0.4447 0.02507 0.3275 0.7978 8.63E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 93 P06168 61 44565 0ILV5_YEAST Ketol-acid reductoisomerase, mitochondrial OS =Saccharomyces cerevisiae GN = ILV5 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 94 P05744 59 12219 0.6527 1RL33A_YEAST 60S ribosomal protein L33-A OS =Saccharomyces cerevisiae GN = RPL33A PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IEGVATPQDAQFYLGK X 0.6527 0.01745 0.2096 0.9659 1.36E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 95 P04807 58 53908 0.6227 1HXKB_YEAST Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 TKYDITIDEESPRPGQQTFEK X 0.6227 0.025240.2555 0.8918 7.65E+04 Hit Accession Score Mass L(L + H) SD(geo) # 96P03965 58 124439 0CARB_YEAST Carbamoyl-phosphate synthase arginine-specific large chain OS =Saccharomyces cerevisiae GN = CPA2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 97 Q00955 58 250197 0ACAC_YEAST Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae GN =FAS3 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 IGSFGPQEDEFFNK 0.8663 0.02199 0.11440.6383 4.24E+05 Hit Accession Score Mass L(L + H) SD(geo) # 98 P32598 5835884 0.499 1 PP12_YEAST Serine/threonine-protein phosphatase PP1-2 OS =Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GSKPGQQVDLEENEIR X 0.499 0.03409 0.1183 0.9862 2959 Hit Accession ScoreMass L(L + H) SD(geo) # 99 P02365 58 27204 0.4787 1RS6_YEAST 40S ribosomal protein S6 OS = Saccharomyces cerevisiae GN =RPS6A PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 KGEQELEGLTDTTVPK X 0.4787 0.014670.0397 0.9854 2.01E+04 Hit Accession Score Mass L(L + H) SD(geo) # 100P37012 57 63049 0 PGM2_YEAST Phosphoglucomutase-2 OS =Saccharomyces cerevisiae GN = PGM2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3IIKDFPELDLGTIGK 0.6291 0.02728 0.1059 0.6921 5.18E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 101 P10664 57 39325 0.482 1.07 2RL4A_YEAST 60S ribosomal protein L4-A OS = Saccharomyces cerevisiae GN =RPL4A PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 IPEIPLVVSTDLESIQK X 0.4871 0.014460.3459 0.9946 8.51E+05 2 3 IINSSEIQSAIRPAGQATQK X 0.4381 0.02184 0.25280.953 9.33E+04 Hit Accession Score Mass L(L + H) SD(geo) # 102 P17536 5523527 0 TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN =TPM1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 QTEQDNVEKENQIK 0.4204 0.1271 0.036150.4953 1.04E+04 2 3 NKDLEQENVEKENQIK 0.438 0.04989 0.1615 0.62216.92E+04 Hit Accession Score Mass L(L + H) SD(geo) # 103 P32469 55 339700 DPH5_YEAST Diphthine synthase OS = Saccharomyces cerevisiae GN =DPH5 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 104 P35271 54 17115 0.5135 1 RS18_YEAST 40S ribosomal protein S18 OS =Saccharomyces cerevisiae GN = RPS18A PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3QNDITDGKDYHTLANNVESK X 0.5135 0.01629 0.07641 0.9441 5.50E+04 HitAccession Score Mass L(L + H) SD(geo) # 105 P13663 54 39735 0DHAS_YEAST Aspartate-semialdehyde dehydrogenase OS =Saccharomyces cerevisiae GN = HOM2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 106 P54839 53 54979 0HMCS_YEAST Hydroxymethylglutaryl-CoA synthase OS =Saccharomyces cerevisiae GN = ERG13 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DYDESLTDKNIEK 0.1337 0.1737 0.3775 0.4027 2.38E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 107 P40016 53 60385 0RPN3_YEAST 26S proteasome regulatory subunit RPN3 OS =Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 108 P05317 52 33866 0.5164 1RLA0_YEAST 60S acidic ribosomal protein P0 OS =Saccharomyces cerevisiae GN = RPP0 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GTIEIVSDVK X 0.5164 0.00778 0.1538 0.9872 4.30E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 109 P15992 51 23865 0HSP26_YEAST Heat shock protein 26 OS = Saccharomyces cerevisiae GN =HSP26 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 NQILVSGEIPSTLNEESKDK 0.6438 0.032780.3187 0.6599 2.01E+05 Hit Accession Score Mass L(L + H) SD(geo) # 110P32481 50 57829 0IF2G_YEAST Eukaryotic translation initiation factor 2 subunit gamma OS =Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LGDEIEIRPGIVTK 0.6051 0.09736 0.2626 0.3614 1.13E+05 2 3VAFTGLEEDGETEEEKR 0.3223 0.05784 0.09351 0.5764 1.71E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 111 P41056 49 12233 0RL33B_YEAST 60S ribosomal protein L33-B OS =Saccharomyces cerevisiae GN = RPL33B PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IEGVATPQEAQFYLGK 0.000032 376.9 0.3763 0.1226 1.13E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 112 P14126 49 44075 0RL3_YEAST 60S ribosomal protein L3 OS = Saccharomyces cerevisiae GN =RPL3 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 113 B3LLJ2 49 29059 0.5829 1RS3A2_YEAS1 40S ribosomal protein S1-B OS =Saccharomyces cerevisiae (strain RM11-1a) GN = RPS1B PE = 3 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 VSGFKDEVLETV X 0.5829 0.0184 0.1617 0.95654.47E+05 Hit Accession Score Mass L(L + H) SD(geo) # 114 P35997 49 89300 RS27A_YEAST 40S ribosomal protein S27-A OS =Saccharomyces cerevisiae GN = RPS27A PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 115 P39954 48 49094 0.1786 1SAHH_YEAST Adenosylhomocysteinase OS = Saccharomyces cerevisiae GN =SAH1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 LKVPAINVNDSVTK X 0.1786 0.1265 0.15370.7426 1.16E+06 Hit Accession Score Mass L(L + H) SD(geo) # 116 P0573648 27392 0.5256 1 RL2_YEAST 60S ribosomal protein L2 OS =Saccharomyces cerevisiae GN = RPL2A PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3ASLNVGNVLPLGSVPEGTIVS X 0.5256 0.00852 0.3563 0.9201 1.23E+06 NVEEKPGDRHit Accession Score Mass L(L + H) SD(geo) # 117 Q12306 47 11662 0SMT3_YEAST Ubiquitin-like protein SMT3 OS =Saccharomyces cerevisiae GN = SMT3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 118 Q14467 47 16394 0.7594 1MBF1_YEAST Multiprotein-bridging factor 1 OS =Saccharomyces cerevisiae GN = MBF1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2INEKPTVVNDYEAAR X 0.7594 0.04153 0.08694 0.7815 1.61E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 119 Q08438 46 73997 0VHS3_YEAST Protein VHS3 OS = Saccharomyces cerevisiae GN = VHS3 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 120 P38708 46 77337 0.3265 1YHI0_YEAST Putative prolyl-tRNA synthetase YHR020W OS =Saccharomyces cerevisiae GN = YHR020W PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IPEILEEMQGDLFK X 0.3265 0.09196 0.1283 0.9662 6.43E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 121 P40069 44 122981 0.8151 1IMB4_YEAST Importin subunit beta-4 OS = Saccharomyces cerevisiae GN =KAP123 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 3 FHEEYLPLIIDIIDSAK X 0.81510.02809 0.2967 0.9444 3.29E+04 Hit Accession Score Mass L(L + H) SD(geo)# 122 P05737 42 27621 0.5221 1RL7A_YEAST 60S ribosomal protein L7-A OS = Saccharomyces cerevisiae GN =RPL7A PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ATLELLK X 0.5221 0.00509 0.1793 0.98718.87E+04 Hit Accession Score Mass L(L + H) SD(geo) # 123 P38715 42 370950.03996 1 GRE3_YEAST NADPH-dependent aldose reductase GRE3 OS =Saccharomyces cerevisiae GN = GRE3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TTPTLFENDVIK X 0.03996 0.4915 0.0985 0.8748 1.48E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 124 P15019 40 37302 0.5972 1TAL1_YEAST Transaldolase OS = Saccharomyces cerevisiae GN = TAL1 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 DYKGEADPGVISVK X 0.5972 0.015130.05713 0.9284 1.93E+04   Hit Accession Score Mass L(L + H) SD(geo) #125 P39939 40 13438 0 RS26B_YEAST 40S ribosomal protein S26-B OS =Saccharomyces cerevisiae GN = RPS26B PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DLSEASVYPEYALPK 0.4244 0.02522 0.09777 0.5891 8.08E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 126 P25443 40 27433 0.4963 1RS2_YEAST 40S ribosomal protein S2 OS = Saccharomyces cerevisiae GN =RPS2 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 EFQIIDTLLPGLQDEVMNIKPV X 0.49630.00439 0.4363 0.9932 1.18E+06 OK Hit Accession Score Mass L(L + H)SD(geo) # 127 P43620 39 75867 0.5908 1RMD8_YEAST Sporulation protein RMD8 OS = Saccharomyces cerevisiae GN =RMD8 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 REQLLK X 0.5908 0.00487 0.1874 0.96965.33E+05 Hit Accession Score Mass L(L + H) SD(geo) # 128 P52910 39 757650 ACS2_YEAST Acetyl-coenzyme A synthetase 2 OS =Saccharomyces cerevisiae GN = ACS2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 129 P60010 38 41663 0ACT_YEAST Actin OS = Saccharomyces cerevisiae GN = ACT1 PE = 1 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 DLTDYLMK 0.8897 0.01324 0.1224 0.6466 4.23E+05 HitAccession Score Mass L(L + H) SD(geo) # 130 P41805 37 25522 0.7348 1RL10_YEAST 60S ribosomal protein L10 OS = Saccharomyces cerevisiae GN =RPL10 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 WGFTNLDRPEYLK X 0.7348 0.02758 0.1070.8056 2.97E+05 Hit Accession Score Mass L(L + H) SD(geo) # 131 Q86ZR737 26338 0 YKD3A_YEAST Putative uncharacterized hydrolase YKL033W-A OS =Saccharomyces cerevisiae GN = YKL033W-A PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 132 P38205 35 77830 0NCL1_YEAST tRNA (cytosine-5-)-methyltransferase NCL1 OS =Saccharomyces cerevisiae GN = NCL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LSSETPALESEGPQTK 0.3404 0.01969 0.1416 0.3584 2.22E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 133 P17255 35 118562 0VATA_YEAST V-type proton ATPase catalytic subunit A OS =Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3AIKEESQSIYIPR 0.2979 0.2188 0.09557 0.4074 1.46E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 134 P05739 35 20183 0.5423 1RL6B_YEAST 60S ribosomal protein L6-B OS = Saccharomyces cerevisiae GN =RPL6B PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 HLEDNTLLVTGPFK X 0.5423 0.02668 0.22650.9184 1.35E+05 Hit Accession Score Mass L(L + H) SD(geo) # 135 Q0753035 34457 0.9709 1YD114_YEAST Uncharacterized oxidoreductase YDL114W OS =Saccharomyces cerevisiae GN = YDL114W PE = 2 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2INRASGTTK X 0.9709 0.00996 0.1262 0.9924 1.27E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 136 P15625 34 57804 0SYFA_YEAST Phenylalanyl-tRNA synthetase alpha chain OS =Saccharomyces cerevisiae GN = FRS2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 137 Q02209 33 41274 0.9909 1YKZ1_YEAST Uncharacterized protein YKR011C OS =Saccharomyces cerevisiae GN = YKR011C PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FQLVEK X 0.9909 0.00329 0.1232 0.9948 5.97E+05 Hit Accession Score MassL(L + H) SD(geo) # 138 A6ZZJ1 32 143286 0.5908 1MYO3_YEAS7 Myosin-3 OS = Saccharomyces cerevisiae (strain YJM789) GN =MYO3 PE = 3 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 RIDAAIK X 0.5908 0.00487 0.1874 0.96965.33E+05 2 3 IIKSANELVETLSK 0.5256 0.06512 0.2213 0.1936 2.39E+05 HitAccession Score Mass L(L + H) SD(geo) # 139 P40077 32 64327 0DSE1_YEAST Protein DSE1 OS = Saccharomyces cerevisiae GN = DSE1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 MNSPILRK 0.003135 3.635 0.06896 0.97847203 Hit Accession Score Mass L(L + H) SD(geo) # 140 A7A1S5 31 76547 0DUS3_YEAS7 tRNA-dihydrouridine synthase 3 OS =Saccharomyces cerevisiae (strain YJM789) GN = DUS3 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations 1 2 QNENQK 0.4468 0.05701 0.00365 0.6454 6837 Hit AccessionScore Mass L(L + H) SD(geo) # 141 P02557 31 51011 0TBB_YEAST Tubulin beta chain OS = Saccharomyces cerevisiae GN =TUB2 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 142 P17423 31 38792 0 KHSE_YEAST Homoserine kinase OS =Saccharomyces cerevisiae GN = THR1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 143 P04076 30 52173 0ARLY_YEAST Argininosuccinate lyase OS = Saccharomyces cerevisiae GN =ARG4 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 144 A6ZWD3 29 68204 0 DBP1_YEAS7 ATP dependent RNA helicase DBP1 OS =Saccharomyces cerevisiae (strain YJM789) GN = DBP1 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations Hit Accession Score Mass L(L + H) SD(geo) # 145 P07702 29 1552480 LYS2_YEAST L-aminoadipate-semialdehyde dehydrogenase OS =Saccharomyces cerevisiae GN = LYS2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EYFVEPNSAEGK 0.0214 0.957 0.3831 0.02822 9.46E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 146 P39976 27 55190 0DLD3_YEAST D-lactate dehydrogenase [cytochrome] 3 OS =Saccharomyces cerevisiae GN = DLD3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LNAAGLIGDAPKPVVK 1 0.00277 0.1741 0.2978 8.97E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 147 P53953 27 98881 0.4536 1SFB2_YEAST SED5-binding protein 2 OS = Saccharomyces cerevisiae GN =SFB2 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 SEQGILNTPK X 0.4536 0.03249 0.30590.9489 4.80E+05 Hit Accession Score Mass L(L + H) SD(geo) # 148 Q0864727 77419 0 PUS7_YEAST Multisubstrate pseudouridine synthase 7 OS =Saccharomyces cerevisiae GN = PUS7 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 149 Q07798 26 102104 0.9876 1SPO75_YEAST Sporulation-specific protein 75 OS =Saccharomyces cerevisiae GN = SPO75 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ILDKIIR X 0.9876 0.00489 0.02083 0.9895 5.42E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 150 P29509 26 34409 0.3208 1TRXB1_YEAST Thioredoxin reductase 1 OS = Saccharomyces cerevisiae GN =TRR1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 IVAGQVDTDEAGYIK X 0.3208 0.064080.4281 0.9649 5.48E+05 Hit Accession Score Mass L(L + H) SD(geo) # 151P38720 26 53774 06PGD1_YEAST 6-phosphogluconate dehydrogenase, decarboxylating 1 OS =Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 152 P26785 26 22444 0RL16B_YEAST 60S ribosomal protein L16-B OS =Saccharomyces cerevisiae GN = RPL16B PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 153 P06843 25 38928 0.5908 1SPT2_YEAST Protein SPT2 OS = Saccharomyces cerevisiae GN = SPT2 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 RQELLK X 0.5908 0.00487 0.1874 0.96965.33E+05 Hit Accession Score Mass L(L + H) SD(geo) # 154 P06101 25 588450.9702 1 CDC37_YEAST Hsp90 co-chaperone Cdc37 OS =Saccharomyces cerevisiae GN = CDC37 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VFEDIPIEEAEK X 0.9702 0.01138 0.1397 0.737 1.27E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 155 P07149 25 228547 0FAS1_YEAST Fatty acid synthase subunit beta OS =Saccharomyces cerevisiae GN = FAS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2WETTTQFK 0.3417 0.07701 0.06965 0.6964 5.87E+04 Hit Accession Score MassL(L + H) SD(geo) # 156 P35169 24 280962 1.001 1TOR1_YEAST Serine/threonine-protein kinase TOR1 OS =Saccharomyces cerevisiae GN = TOR1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EIKFIK X 1.001 0 0.1891 0.9934 1.08E+05 Hit Accession Score Mass L(L +H) SD(geo) # 157 Q05016 24 29301 0YM71_YEAST Uncharacterized oxidoreductase YMR226C OS =Saccharomyces cerevisiae GN = YMR226C PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3IKPFIENLPQEFK 0.4711 0.02328 0.1926 0.2766 5.31E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 158 P23796 24 59181 0RIT1_YEAST tRNA A64-2′-O-ribosylphosphate transferase OS =Saccharomyces cerevisiae GN = RIT1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LNELFMGK 0.173 0.1599 0.1023 0.6886 5.41E+04 Hit Accession Score MassL(L + H) SD(geo) # 159 Q12734 23 124772 0.9979 1CSR2_YEAST Transcription factor CSR2 OS = Saccharomyces cerevisiae GN =CSR2 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 STTLSDIK X 0.9979 0 0.5316 0.99923.05E+06 Hit Accession Score Mass L(L + H) SD(geo) # 160 P24384 23130674 0.5908 1PRP22_YEAST Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22OS = Saccharomyces cerevisiae GN = PRP22 PE = 1 SV = 1 Modifi- zSequence Incl. L(L + H) Std. Err. Fraction Correlation Intensity cations1 2 ERALGIK X 0.5908 0.00487 0.1874 0.9696 5.33E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 161 Q04412 23 54780 0.9523 1AGE1_YEAST ADP-ribosylation factor GTPase-activating protein effector protein 1OS = Saccharomyces cerevisiae GN = AGE1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LTNILLK X 0.9523 0.00751 0.01207 0.9072 1.83E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 162 P53191 22 70950 0PIB2_YEAST Phosphatidylinositol-3-phosphate-binding protein 2 OS =Saccharomyces cerevisiae GN = PIB2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 163 Q03497 22 102940 1 1STE20_YEAST Serine/threonine-protein kinase STE20 OS =Saccharomyces cerevisiae GN = STE20 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ETLSGLEFLHSK X 1 0.00609 0.6136 0.9975 1.27E+06 Hit Accession Score MassL(L + H) SD(geo) # 164 P40462 22 107655 0.9911 1TM108_YEAST Protein TMA108 OS = Saccharomyces cerevisiae GN =TMA108 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 2 FINLEK X 0.9911 0.00377 0.1220.9964 5.91E+05 Hit Accession Score Mass L(L + H) SD(geo) # 165 P0575522 22285 0 RS9B_YEAST 40S ribosomal protein S9-B OS =Saccharomyces cerevisiae GN = RPS9B PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LDYVLALK 0.005702 1.64 0.079 0.8879 9978 Hit Accession Score Mass L(L +H) SD(geo) # 166 P46679 22 97766 0 STB2_YEAST Protein STB2 OS =Saccharomyces cerevisiae GN = STB2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3SSLQGQGKTGICSAIDPKSDK 0.9544 0.00932 0.1894 0.3151 7.47E+05 HitAccession Score Mass L(L + H) SD(geo) # 167 POCOW1 22 14705 0RS22A_YEAST 40S ribosomal protein S22-A OS =Saccharomyces cerevisiae GN = RPS22A PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 168 P36096 22 88064 0.9908 1TUL1_YEAST Transmembrane E3 ubiquitin-protein ligase 1 OS =Saccharomyces cerevisiae GN = TUL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IDLVSNNK X 0.9908 0.00823 0.03719 0.9728 1.54E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 169 P38967 21 65362 0TAT2_YEAST Tryptophan permease OS = Saccharomyces cerevisiae GN =TAT2 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 170 Q05955 21 57795 0.8578 1ADY4_YEAST Accumulatesd yads protein 4 OS =Saccharomyces cerevisiae GN = ADY4 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DVDYQTFK X 0.8578 0.03111 0.08023 0.9212 1.78E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 171 P26786 21 21761 0RS7A_YEAST 40S ribosomal protein S7-A OS = Saccharomyces cerevisiae GN =RPS7A PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 172 P18759 21 84004 1 1SEC18_YEAST Vesicular-fusion protein SEC18 OS =Saccharomyces cerevisiae GN = SEC18 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FKIPGFGK X 1 0.00372 0.3628 0.9814 2.01E+05 Hit Accession Score MassL(L + H) SD(geo) # 173 P02309 21 11361 0.4287 1 H4_YEAST Histone H4 OS =Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DSVTYTEHAK X 0.4287 0.05722 0.06178 0.844 1.78E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 174 P36139 20 31428 0PET10_YEAST Protein PET10 OS = Saccharomyces cerevisiae GN = PET10 PE =1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LDELVNLLVFK 0.001257 0.6587 0.76850.9993 1.17E+06 Hit Accession Score Mass L(L + H) SD(geo) # 175 Q0277320 140029 1RPM2_YEAST Ribonuclease P protein component, mitochondrial OS =Saccharomyces cerevisiae GN = RPM2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SLLRKSKPLQA X 0 999 0.00047 0.8095 271.1 Hit Accession Score Mass L(L +H) SD(geo) # 176 P38697 20 56494 0.3128 1IMDH2_YEAST Inosine-5′-monophosphate dehydrogenase IMD2 OS =Saccharomyces cerevisiae GN = IMD2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3TASAQLEGGVHNLHSYEK X 0.3128 0.09825 0.218 0.8306 1.40E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 177 P41832 20 221017 0.02392 1BNI1_YEAST Protein BNI1 OS = Saccharomyces cerevisiae GN = BNI1 PE =1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 RLKELETK X 0.02392 0.2888 0.005470.8577 1621 Hit Accession Score Mass L(L + H) SD(geo) # 178 P17119 2083952 0.09389 1 KAR3_YEAST Kinesin-like protein KAR3 OS =Saccharomyces cerevisiae GN = KAR3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TNLETLEK X 0.09389 0.2254 0.0084 0.9135 5.14E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 179 P15303 20 85579 0SEC23_YEAST Protein transport protein SEC23 OS =Saccharomyces cerevisiae GN = SEC23 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 180 P32565 20 104768 0RPN2_YEAST 26S proteasome regulatory subunit RPN2 OS =Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 181 Q03660 20 128787 0TR130_YEAST Transport protein particle 130 kDa subunit OS =Saccharomyces cerevisiae GN = TRS130 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 182 P39081 19 71853 0PCF11_YEAST Protein PCF11 OS = Saccharomyces cerevisiae GN = PCF11 PE =1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 INNLYASLKAEGLIYTPPK 0.9323 0.014020.3541 0.6434 6.37E+04 Hit Accession Score Mass L(L + H) SD(geo) # 183B3LRC2 19 36810 0 UTH1_YEAS1 Protein UTH1 OS =Saccharomyces cerevisiae (strain RM11-1a) GN = UTH1 PE = 3 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations Hit Accession Score Mass L(L + H) SD(geo) # 184 P0725919 244972 0 PYR1_YEAST Protein URA1 OS = Saccharomyces cerevisiae GN =URA2 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 185 P18963 19 350758 0.9999 1IRA1_YEAST Inhibitory regulator protein IRA1 OS =Saccharomyces cerevisiae GN = IRA1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GNKYLIK X 0.9999 0.00158 0.0893 0.9713 3.78E+04 Hit Accession Score MassL(L + H) SD(geo) # 186 P38850 18 123854 0RT107_YEAST Regulator of Ty1 transposition protein 107 OS =Saccharomyces cerevisiae GN = RTT107 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 187 Q04199 18 51420 0CAC2_YEAST Chromatin assembly factor 1 subunit p60 OS =Saccharomyces cerevisiae GN = CAC2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IPCNSSDSK 0.9943 0.00328 0.1865 0.52 1.44E+06 Hit Accession Score MassL(L + H) SD(geo) # 188 Q12345 17 28402 0IES3_YEAST Ino eighty subunit 3 OS = Saccharomyces cerevisiae GN =IE53 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 IDILTKIQENLLEEYQK 0.04155 1.4170.06472 0.5595 1068 Hit Accession Score Mass L(L + H) SD(geo) # 189P53598 17 35010 1.001 1 SUCA_YEAST Succinyl-CoA ligase [ADP-forming]subunit alpha, mitochondrial OS = Saccharomyces cerevisiae GN =LSC1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ESIPYDK X 1.001 0.001 0.6215 0.99593.11E+06

TABLE 2Proteins identified by Mascot Distiller from ChAP-MS analysis of GAL1 chromatin isolated from cellsgrown in galactose. Mascot Distiller Quantitation ReportMascot search results: Galactose Log ratio versus Log ratio versusIntensity (all Intensity (selected positive ratios) ratios) L/ 02.00e+705.00e+6 (L + 4.00e+7 6.00e+7 1.00e+7 1.50e+7 H) −15 −10 −5 0 5−6 −4 −2 0 2 Hit Accession Score Mass L(L + H) SD(geo) # 1 P00924 95246773 0.727 1.077 10 ENO1_YEAST Enolase 1 OS =Saccharomyces cerevisiae GN = ENO1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2RIATAIEK X 0.9922 0.001 0.0623 0.9937 78080.00 2 2 VNQIGTLSESIK X 0.72370.001 0.6107 0.9971 1.48E+06 3 3 AVDDFLISLDGTANK X 0.6953 0.00258 0.56050.9825 2.57E+05 4 2 AVDDFLISLDGTANK X 0.678 0.00158 0.1606 0.98393.20E+06 5 2 TAGIQIVADDLTVTNPK X 0.8499 0 0.4502 0.9983 8.74E+05 6 3IEEELGDNAVFAGENFHHGDK X 0.7139 0.01531 0.04418 0.7314 3.10E+04 7 2IEEELGDNAVFAGENFHHGDKL X 0.8709 0.00321 0.8165 0.9933 1.28E+05 8 3IEEELGDNAVFAGENFHHGDKL X 0.8482 0.00579 0.7751 0.9956 5.69E+05 9 3YPIVSIEDPFAEDDWEAWSHFFK X 0.743 0.001 0.7934 0.9984 1.74E+06 10 3RYPIVSIEDPFAEDDWEAWSHFFK 0.2589 0.1734 0.2248 0.5408 1353 11 3YGASAGNVGDEGGVAPNIQTAEE X 0.7223 0.00158 0.9201 0.9993 1.05E+07ALDLIVDAIK SD Hit Accession Score Mass L(L + H) (geo) # 2 P00925 82746885 0.7156 1.024 5 ENO2_YEAST Enolase 2 OS =Saccharomyces cerevisiae GN = ENO2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VNQIGTLSESIK X 0.7237 0.001 0.6107 0.9971 1.48E+06 2 3 AVDDFLLSLDGTANK X0.6953 0.00258 0.5605 0.9825 2.57E+05 3 2 AVDDFLLSLDGTANK X 0.6780.00158 0.1606 0.9839 3.20E+06 4 2 DGKYDLDFKNPESDK 0.593 0.03836 0.25150.6481 3.31E+05 5 3 DGKYDLDFKNPESDK 0.2183 0.1283 0.2233 0.1889 8.04E+056 3 YPIVSIEDPFAEDDWEAWSHFFK X 0.743 0.001 0.7934 0.9984 1.74E+06 7 3RYPIVSIEDPFAEDDWEAWSHFFK 0.2589 0.1734 0.2248 0.5408 1353 8 3YGASAGNVGDEGGVAPNIQTAEE X 0.7223 0.00158 0.9201 0.9993 1.05E+07ALDLIVDAIK SD Hit Accession Score Mass L(L + H) (geo) # 3 P00359 77335724 0.6771 1.019 7G3P3_YEAST Glyceraldehyde-3-phosphate dehydrogenase 3 OS =Saccharomyces cerevisiae GN = TDH3 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3ETTYDEIKK X 0.6838 0.00472 0.3538 0.9553 3.68E+05 2 2 TASGNIIPSSTGAAK X0.6648 0.00158 0.6513 0.9983 3.86E+06 3 2 VPTVDVSVVDLTVK X 0.7282 0.00640.2127 0.8286 6.60E+05 4 3 LNKETTYDEIKK 0.7548 0.04527 0.0313 0.20685.04E+04 5 3 YAGEVSHDDKHIIVDGK 0.688 0.0049 0.1652 0.6807 4.07E+06 6 2YAGEVSHDDKHIIVDGK X 0.6826 0.00224 0.3878 0.8652 2.07E+06 7 3KVVITAPSSTAPMFVMGVNEEK X 0.7193 0.00631 0.1023 0.9512 2.42E+05 8 2DPANLPWGSSNVDIAIDSTGVFK X 0.6776 0.00494 0.5179 0.9695 1.47E+06 9 3DPANLPWGSSNVDIAIDSTGVFK 0.6946 0.02605 0.3559 0.4268 1.47E+06 10 3VINDAFGIEEGLMTTVHSLTATQK X 0.6612 0.0114 0.3918 0.9512 5.69E+05 SD HitAccession Score Mass L(L + H) (geo) # 4 P02994 662 50394 0.8504 1.012 7EF1A_YEAST Elongation factor 1-alpha OS = Saccharomyces cerevisiae GN =TEF1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 FDELLEK X 0.826 0.00158 0.3074 0.99234.71E+06 2 3 SHINVVVIGHVDSGK 0.8651 0.00919 0.1342 0.4249 1.91E+05 3 2TLLEAIDAIEQPSRPTDKPLR X 0.8558 0 0.7243 0.9974 1.11E+06 4 3TLLEAIDAIEQPSRPTDKPLR X 0.8371 0.00322 0.6393 0.9893 8.82E+06 5 3VETGVIKPGMVVTFAPAGVTTEVK X 0.8774 0.001 0.7139 0.9992 6.53E+06 6 2VETGVIKPGMVVTFAPAGVTTEVK X 0.8911 0 0.7784 0.9982 2.27E+06 7 3SVEMHHEQLEQGVPGDNVGFNV X 0.8474 0.00071 0.7764 0.9988 1.10E+07 K 8 2SVEMHHEQLEQGVPGDNVGFNV X 0.8482 0.001 0.8709 0.999 1.09E+06 K HitAccession Score Mass L(L + H) SD(geo) # 5 P54115 486 54380 0.6881 1.0245 ALDH6_YEAST Magnesium-activated aldehyde dehydrogenase, cytosolic OS =Saccharomyces  cerevisiae GN = ALD6 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SVAVDSSESNLK X 0.7081 0.0109 0.05156 0.971 5.45E+05 2 3 SVAVDSSESNLKK X0.6272 0.01694 0.1014 0.9286 2.04E+05 3 2 SVAVDSSESNLKK X 0.6886 0.001580.2331 0.997 7.45E+05 4 3 SAHLVFDDANIKK X 0.6792 0.004 0.1402 0.95962.03E+05 5 3 IVKEEIFGPVVTVAK 0.2547 0.07849 0.4923 0.06903 3.53E+06 6 2IVKEEIFGPVVTVAK X 0.6996 0.00158 0.1833 0.9947 3.23E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 6 P10591 482 70039 0.8188 1.018 4HSP71_YEAST Heat shock protein SSA1 OS = Saccharomyces cerevisiae GN =SSA1 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 MKETAESYLGAK X 0.7735 0.00986 0.26920.9866 2.32E+05 2 2 NFNDPEVQADMK X 0.8218 0.00856 0.2133 0.9657 9.80E+053 2 NQAAMNPSNTVFDAK X 0.8186 0.0035 0.4594 0.9975 1.37E+06 4 3NTISEAGDKLEQADKDTVTK 0.3583 0.06491 0.4424 0.4808 1.01E+07 5 2NTISEAGDKLEQADKDTVTK X 0.8301 0.00158 0.6157 0.995 7.24E+05 SD HitAccession Score Mass L(L + H) (geo) # 7 P50095 425 56813 0.9382 1.024 5IMDH3_YEAST Probable inosine-5′-monophosphate dehydrogenase IMD3 OS =Saccharomyces  cerevisiae GN = IMD3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3TASAQLEGGVHNLHSYEK 0.4222 0.1268 0.5294 0.3116 7.78E+05 2 2TASAQLEGGVHNLHSYEK X 0.893 0.02366 0.2283 0.9113 2.44E+05 3 2NPVTGAQGITLSEGNEILK X 0.9433 0.00754 0.3647 0.9924 1.01E+06 4 3NPVTGAQGITLSEGNEILK X 0.9335 0.00158 0.3228 0.9933 3.39E+05 5 2YFSESDSVLVAQGVSGAVVDK X 1 0.001 0.4121 0.9864 7.24E+04 6 2GGLTYNDFLVLPGLVDFPSSEVSL X 0.9534 0 0.8179 0.9932 2.35E+05 QTK SD HitAccession Score Mass L(L + H) (geo) # 8 P07262 383 49539 0.5666 1.061 3DHE4_YEAST NADP-specific glutamate dehydrogenase 1 OS =Saccharomyces cerevisiae GN = GDH1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2STATGPSEAVWYGPPK X 0.6132 0.00959 0.3565 0.9733 2.44E+05 2 3VTWENDKGEQEVAQGYR X 0.535 0.02836 0.5322 0.8087 5.75E+05 3 2VTWENDKGEQEVAQGYR X 0.6306 0.00328 0.4773 0.9937 1.29E+05 SD HitAccession Score Mass L(L + H) (geo) # 9 P06169 369 61737 0.5627 5PDC1_YEAST Pyruvate decarboxylase isozyme 1 OS =Saccharomyces cerevisiae GN = PDC1 PE = 1 SV = 7 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VATTGEWDKLTQDK X 0.5604 0.00308 0.3782 0.9946 8.35E+05 2 3YGGVYVGTLSKPEVK X 0.5512 0.00325 0.3138 0.9816 4.29E+05 3 2YGGVYVGTLSKPEVK X 0.5578 0.001 0.3925 0.9961 8.00E+05 4 3LLQTPIDMSLKPNDAESEK X 0.6389 0.08423 0.3737 0.9119 2000 5 2MIEIMLPVFDAPQNLVEQAK X 0.6331 0.00453 0.5965 0.979 1.63E+05 SD HitAccession Score Mass L(L + H) (geo) # 10 P29311 363 30209 0.7744 1.108 3BMH1_YEAST Protein BMH1 OS = Saccharomyces cerevisiae GN = BMH1 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 QAFDDAIAELDTLSEESYK X 0.7998 0.002550.5395 0.9946 4.35E+05 2 2 ISDDILSVLDSHLIPSATTGESK X 0.625 0.01278 0.2710.7283 1.76E+05 3 3 ISDDILSVLDSHLIPSATTGESK X 0.7868 0.00158 0.17460.9972 1.49E+06 Hit Accession Score Mass L(L + H) SD(geo) # 11 P15108361 81435 0.007455 6HSC82_YEAST ATP-dependent molecular chaperone H5C82 OS =Saccharomyces cerevisiae GN = HSC82 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2AILFIPK X 0.7304 0.00664 0.3427 0.9954 5.12E+04 2 2 RVDEGGAQDK X 0.7340.007 0.04224 0.965 9084 3 2 KDEDDKKPK 0.4443 0.1702 0.04474 0.339 22024 2 ALKDILGDQVEK X 0.7398 0.01231 0.03927 0.8976 8.40E+04 5 3VKEEVQELEELNK X 0.711 0.00306 0.1697 0.9942 2.85E+05 6 2 LEEVDEEEEEKKPKX 0.6241 0.03842 0.06528 0.873 2.25E+05 7 3 TLVDITKDFELEETDEEKAER X0.005607 0.09361 0.4759 0.9104 1.04E+07 SD Hit Accession Score MassL(L + H) (geo) # 12 P46655 353 81369 0.8084 4SYEC_YEAST Glutamyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = GUS1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ANFEIDLPDAK X 0.8028 0.00578 0.1682 0.9743 6.26E+05 2 2 IHLEGSEAPQEPK X0.8001 0.01046 0.2506 0.9636 5.39E+05 3 3 EKEEFQDSILEDLDLLGIK X 0.82580.00576 0.2679 0.9657 5.87E+05 4 2 EKEEFQDSILEDLDLLGIK X 0.7985 0.004410.3707 0.9948 1.96E+05 Hit Accession Score Mass L(L + H) SD(geo) # 13P32589 346 77318 0.7318 1.014 3HSP7F_YEAST Heat shock protein homolog SSE1 OS =Saccharomyces cerevisiae GN = SSE1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EELEELVKPLLER X 0.7536 0.03052 0.07918 0.8999 7.17E+04 2 2GKLEEEYAPFASDAEK 0.6193 0.01623 0.1684 0.5929 1.11E+06 3 2IIGLDYHHPDFEQESK X 0.7328 0.01091 0.08547 0.9763 8.03E+04 4 3QVEDEDHMEVFPAGSSF X 0.7218 0.01002 0.3701 0.8889 1.59E+05 PSTK HitAccession Score Mass L(L + H) SD(geo) # 14 P00560 322 44711 0.5639 1.4483 PGK_YEAST Phosphoglycerate kinase OS = Saccharomyces cerevisiae GN =PGK1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 VDFNVPLDGK X 0.272 0.04331 0.30240.8665 1.97E+06 2 2 VLENTEIGDSIFDK 0.9987 0 0.8558 0.2984 5.35E+07 3 2SSAAGNTVIIGGGDTATV X 0.7606 0.00838 0.6009 0.9775 2.98E+06 AK 4 2GVEVVLPVDFIIADAFSAD X 0.8169 0.00271 0.6174 0.9986 1.47E+06 ANTK HitAccession Score Mass L(L + H) SD(geo) # 15 P00549 296 54807 0.7976 1.0255 KPYK1_YEAST Pyruvate kinase 1 OS = Saccharomyces cerevisiae GN =PYK1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 MNFSHGSYEYHK X 0.7461 0.02847 0.16140.8404 2.71E+05 2 2 MNFSHGSYEYHK X 0.8117 0.00999 0.1068 0.9731 4.19E+053 2 GVNLPGTDVDLPALSEK X 0.8043 0.00272 0.5459 0.9882 6.30E+06 4 2GDLGIEIPAPEVLAVQK X 0.7994 0.001 0.5602 0.9987 7.61E+06 5 2SEELYPGRPLAIALDTK 0.002097 3.304 0.1291 0.6758 1.89E+05 6 3KSEELYPGRPLAIALDTK X 0.7575 0.00877 0.1331 0.7972 1.12E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 16 P38720 295 53509 0.9328 1.029 46PGD1_YEAST 6-phosphogluconate dehydrogenase, decarboxylating 1 OS =Saccharomyces  cerevisiae GN = GND1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SIIGATSIEDFISK X 0.9129 0.001 0.1873 0.9973 1.68E+05 2 3 LGGFTDKEISDVFAKX 0.949 0.00158 0.2086 0.9846 6.26E+05 3 2 AYREEPDLENLLFNK X 0.9360.00484 0.3345 0.723 3.06E+06 4 3 YGPSLMPGGSEEAWPHI X 0.8712 0.005610.3785 0.9595 2.62E+05 K Hit Accession Score Mass L(L + H) SD(geo) # 17P04385 290 57907 0.6139 1.13 4 GAL1_YEAST Galactokinase OS =Saccharomyces cerevisiae GN = GAL1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NPSITLINADPK X 0.7365 0.001 0.5381 0.9953 2.36E+06 2 3 MLVLVEESLANKK X0.7882 0.0105 0.2982 0.9203 2.53E+05 3 2 SHSEEVIVPEFNSSAK X 0.53770.04126 0.3609 0.9033 3.79E+06 4 2 VLNEKNPSITLINADPK X 0.7577 0.003420.1352 0.9951 4.28E+04 Hit Accession Score Mass L(L + H) SD(geo) # 18P04397 264 78146 0.6778 7 GAL10_YEAST Bifunctional protein GAL10 OS =Saccharomyces cerevisiae GN = GAL10 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 1LEVLTK X 0.8734 0.001 0.01287 0.9936 9.32E+04 2 2 DYIHVVDLAK X 0.86140.00158 0.2342 0.9952 1.38E+06 3 3 DYIHVVDLAK X 0.9574 0 0.4691 0.95784.66E+05 4 2 AGDVLNLTAKPDR X 0.8088 0.00531 0.07739 0.9941 4.67E+05 5 2EIATFNSTKPTVLGPK X 1.003 0.01104 0.02312 0.9843 1.39E+04 6 2YAIENILNDLYNSDK X 0.5331 0.02963 0.3656 0.7372 2.83E+06 7 2SVDVDKNMIPTGNIVDR X 0.8696 0.00158 0.2804 0.9956 3.03E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 19 P11484 262 66561 0.8176 1.003 3HSP75_YEAST Heat shock protein SSB1 OS = Saccharomyces cerevisiae GN =SSB1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LLSDFFDGK X 0.8188 0.001 0.534 0.9989.62E+05 2 2 RFDDESVQK X 0.8212 0.00341 0.3458 0.9841 1.10E+06 3 2ENTLLGEFDLK X 0.8144 0.00158 0.4074 0.9981 1.59E+06 Hit Accession ScoreMass L(L + H) SD(geo) # 20 P08431 261 42358 0.6343 8.653 3GAL7_YEAST Galactose-1-phosphate uridylyltransferase OS =Saccharomyces cerevisiae GN = GAL7 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3EHNTDLFADYVK X 0.01158 0.4988 0.2836 0.9602 5.87E+05 2 2LDQPILPQNDSNEDNLK X 0.918 0 0.8548 0.9997 6.17E+06 3 3 RPWLGQQEAAYKPTAPLX 0.7836 0.01208 0.1133 0.9209 3.76E+05 YDPK Hit Accession Score MassL(L + H) SD(geo) # 21 Q01560 247 45444 0NOP3_YEAST Nucleolar protein 3 OS = Saccharomyces cerevisiae GN =NPL3 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 22 P07284 238 53677 0.2383 4SYSC_YEAST Seryl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = SES1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YIPGEPEFLPFVNELPK X 0.8227 0.00158 0.4653 0.9473 1.11E+05 2 3NASVEIVDEIISDYKDWVK X 0.7951 0.00573 0.4831 0.9887 3.44E+05 3 2NASVEIVDEIISDYKDWVK X 0.7696 0.01392 0.1984 0.9426 6.67E+04 4 3IEQFVITEPEKSWEEFEK X 0.114 0.1522 0.1374 0.9075 8.56E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 23 P38088 234 75364 0.8224 1.006 2SYG_YEAST Glycyl-tRNA synthetase 1 OS = Saccharomyces cerevisiae GN =GRS1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 IDDSGVSIGK X 0.8259 0.01171 0.17810.9752 4.43E+05 2 2 LDDDVVKEYEEILAK X 0.8161 0.01051 0.07847 0.96582.44E+05 Hit Accession Score Mass L(L + H) SD(geo) # 24 P17709 225 553420.1024 15.72 2 HXKG_YEAST Glucokinase-1 OS =Saccharomyces cerevisiae GN = GLK1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EGHTLASDK X 0.003844 0.1695 0.7656 0.9015 6.01E+05 2 2 YDVVIDQK X 0.8360.0107 0.2711 0.9649 9.39E+05 Hit Accession Score Mass L(L + H) SD(geo)# 25 P10592 223 69844 0.6324 1.099 3HSP72_YEAST Heat shock protein SSA2 OS = Saccharomyces cerevisiae GN =SSA2 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 MKETAESYLGAK X 0.7735 0.00986 0.26920.9866 2.32E+05 2 2 NFNDPEVQGDMK X 0.5921 0.01773 0.3417 0.9151 3.96E+053 3 NTISEAGDKLEQADKDAV X 0.6179 0.00324 0.3113 0.9818 8.87E+05 TK HitAccession Score Mass L(L + H) SD(geo) # 26 P34760 203 21688 0.8525 1TSA1_YEAST Peroxiredoxin TSA1 OS = Saccharomyces cerevisiae GN =TSA1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 TAVVDGVFDEVSLDK X 0.8525 0.003 0.23040.9765 1.37E+06 Hit Accession Score Mass L(L + H) SD(geo) # 27 P07806202 126596 0.902 1.08 2SYV_YEAST Valyl-tRNA synthetase, mitochondrial OS =Saccharomyces cerevisiae GN = VAS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TAEDQKDSIVSLIK X 0.8245 0.0142 0.06813 0.9834 6.02E+04 2 2TGEVIINPLKEDGSPK X 0.9585 0.02748 0.09926 0.894 8.93E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 28 P39015 200 29977 0.8734 1.037 2STM1_YEAST Suppressor protein STM1 OS = Saccharomyces cerevisiae GN =STM1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 TAQLSLQDYLNQQANNQ X 0.9037 0.01590.345 0.8549 1.14E+05 FNK 2 2 EAQADAAAEIAEDAAEAE X 0.8405 0.03245 0.26660.956 1.01E+05 DAGKPK Hit Accession Score Mass L(L + H) SD(geo) # 29P14540 196 39596 0.7378 1.02 2ALF_YEAST Fructose-bisphosphate aldolase OS =Saccharomyces cerevisiae GN = FBA1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GISNEGQNASIK X 0.7232 0.00563 0.2971 0.9957 2.70E+06 2 2LLPWFDGMLEADEAYFK X 0.7527 0.00701 0.6657 0.9971 2.69E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 30 P07259 183 245990 0.6064 1PYR1_YEAST Protein URA1 OS = Saccharomyces cerevisiae GN = URA2 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 SISGPVITDVASLK X 0.6064 0.036810.07372 0.792 2.43E+05 Hit Accession Score Mass L(L + H) SD(geo) # 31P16521 177 115920 0.7059 1.311 3 EF3A_YEAST Elongation factor 3A OS =Saccharomyces cerevisiae GN = YEF3 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TQLRLKR X 0.9013 0.00444 0.3845 0.99 2.38E+06 2 2 AYEELSNTDLEFK X 0.79970.02628 0.5649 0.9771 1.97E+06 3 3 AYEELSNTDLEFKFPEPG X 0.3863 0.031750.257 0.8484 1.37E+06 YLEGVK Hit Accession Score Mass L(L + H) SD(geo) #32 P11412 168 57830 0.5867 1.242 2G6PD_YEAST Glucose-6-phosphate 1-dehydrogenase OS =Saccharomyces cerevisiae GN = ZWF1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2AVAPIDTDDVLLGQYGK X 0.5629 0.04227 0.2849 0.9375 7.08E+05 2 3SEDGSKPAYVDDDTVDK X 0.7949 0.00856 0.1299 0.9748 9.45E+04 DSK HitAccession Score Mass L(L + H) SD(geo) # 33 P07149 160 228547 0.8094 1FAS1_YEAST Fatty acid synthase subunit beta OS =Saccharomyces cerevisiae GN = FAS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GNYTDFENTFQK X 0.8094 0.01799 0.0845 0.9521 3.39E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 34 P28240 159 62369 0.3227 1ACEA_YEAST Isocitrate lyase OS = Saccharomyces cerevisiae GN = ICL1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LDADAAEIEK X 0.3227 0.07711 0.2020.9617 8.83E+05 Hit Accession Score Mass L(L + H) SD(geo) # 35 P00330155 36800 0.8664 1.009 3 ADH1_YEAST Alcohol dehydrogenase 1 OS =Saccharomyces cerevisiae GN = ADH1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VVGLSTLPEIYEK X 0.8678 0.00158 0.5758 0.9962 2.12E+06 2 2VLGIDGGEGKEELFR X 0.8513 0.00158 0.397 0.9977 2.05E+06 3 3VLGIDGGEGKEELFR X 0.8778 0.00344 0.5496 0.9935 2.51E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 36 P32527 155 48990 0.8655 1ZUO1_YEAST Zuotin OS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 3 ATTIDEQVGLIVDSLNDEE X 0.8655 0.00448 0.4525 0.96132.75E+05 LVSTADK Hit Accession Score Mass L(L + H) SD(geo) # 37 P04806155 53705 0.8304 1 HXKA_YEAST Hexokinase-1 OS =Saccharomyces cerevisiae GN = HXK1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LSGNHTFDTTQSK 0.1191 0.209 0.1488 0.6634 3.26E+05 2 3 TKYDVAVDEQSPRPGQQX 0.8304 0.01169 0.1392 0.9589 2.37E+04 AFEK Hit Accession Score MassL(L + H) SD(geo) # 38 P05750 153 26486 0.7359 1R53_YEAST 40S ribosomal protein S3 OS = Saccharomyces cerevisiae GN =RPS3 PE = 1 SV = 5 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 ALPDAVTIIEPKEEEPILAP X 0.7359 0.012510.06703 0.9895 3.55E+05 SVK Hit Accession Score Mass L(L + H) SD(geo) #39 P53252 152 38486 0.8196 1PIL1_YEAST Sphingolipid long chain base-responsive protein PIL1 OS =Saccharomyces  cerevisiae GN = PIL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2APTASQLQNPPPPPSTTK X 0.8196 0.01915 0.2011 0.9301 1.74E+05 2 3ALLELLDDSPVTPGETRP 0.6536 0.03193 0.2367 0.6395 5.49E+05 AYDGYEASK HitAccession Score Mass L(L + H) SD(geo) # 40 P00817 151 32280 0.467 4IPYR_YEAST Inorganic pyrophosphatase OS = Saccharomyces cerevisiae GN =IPP1 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 LNDIEDVEK X 0.3227 0.07711 0.2020.9617 8.83E+05 2 3 LEITKEETLNPIIQDTK X 0.736 0.01106 0.2893 0.93144.97E+05 3 3 AVGDNDPIDVLEIGETIAY X 0.7062 0.00365 0.6552 0.992 1.59E+05TGQVK 4 2 AVGDNDPIDVLEIGETIAY X 0.741 0.002 0.7827 0.9921 7.42E+04 TGQVKHit Accession Score Mass L(L + H) SD(geo) # 41 Q03048 144 15891 0COFI_YEAST Cofilin OS = Saccharomyces cerevisiae GN = COF1 PE = 1 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 SGVAVADESLTAFNDLK 0.519 0.05769 0.1215 0.59823.04E+05 Hit Accession Score Mass L(L + H) SD(geo) # 42 P32324 142 932300.7058 3 EF2_YEAST Elongation factor 2 OS =Saccharomyces cerevisiae GN = EFT1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3WTNKDTDAEGKPLER X 0.7908 0.00868 0.07043 0.8558 2.83E+05 2 2WTNKDTDAEGKPLER X 0.1675 0.2545 0.2121 0.7622 2.57E+05 3 3GQVVSEEQRPGTPLFTV X 0.8025 0.001 0.5728 0.9927 2.98E+06 K Hit AccessionScore Mass L(L + H) SD(geo) # 43 A6ZP47 141 65697 0DED1_YEAS7 ATP-dependent RNA helicase DED1 OS =Saccharomyces cerevisiae (strain YJM789) GN = DED1 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations 1 2 DVPEPITEFTSPPLDGLLL 0.00021 5.488 0.7663 0.08765 2.92E+06ENIK Hit Accession Score Mass L(L + H) SD(geo) # 44 P22515 139 1141950.756 1 UBA1_YEAST Ubiquitin-activating enzyme E11 OS =Saccharomyces cerevisiae GN = UBA1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SDDSNSKPNVDEYK X 0.756 0.02454 0.07431 0.9725 4.83E+04 2 2QFMYFDSLESLPDPK 0.000528 7.296 0.0675 0.6501 1.43E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 45 P38701 137 14011 0.6173 1R520_YEAST 40S ribosomal protein S20 OS = Saccharomyces cerevisiae GN =RPS20 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 EKVEEQEQQQQQIIK X 0.6173 0.007340.2134 0.9546 6.58E+05 Hit Accession Score Mass L(L + H) SD(geo) # 46P14742 133 80357 0GFA1_YEAST Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]OS = Saccharomyces cerevisiae GN = GFA1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 47 P22768 133 47175 0ASSY_YEAST Argininosuccinate synthase OS = Saccharomyces cerevisiae GN =ARG1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 48 P10664 131 39325 0.7018 1.054 3RL4A_YEAST 60S ribosomal protein L4-A OS = Saccharomyces cerevisiae GN =RPL4A PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 IPEIPLVVSTDLESIQK X 0.7524 0.006930.3528 0.9385 3.17E+05 2 2 IPEIPLVVSTDLESIQK X 0.6885 0.00408 0.49630.9979 7.46E+05 3 3 IINSSEIQSAIRPAGQATQ X 0.6478 0.00324 0.4073 0.99479.65E+04 K Hit Accession Score Mass L(L + H) SD(geo) # 49 P35691 12818849 0.8547 1TCTP_YEAST Translationally-controlled tumor protein homolog OS =Saccharomyces cerevisiae GN = TMA19 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DIFSNDELLSDAYDAK X 0.8547 0.00941 0.2439 0.9901 9.80E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 50 P15303 127 85331 0SEC23_YEAST Protein transport protein 5EC23 OS =Saccharomyces cerevisiae GN = SEC23 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FFLPLEQVEFK 0.7553 0.01157 0.2147 0.5191 1.45E+05 2 2 KAGYQDDPQYADFK0.9927 0.02465 0.1877 0.3964 5.07E+04 Hit Accession Score Mass L(L + H)SD(geo) # 51 Q03690 124 145076 0.5813 1 TIF31_YEAST Protein TIF31 OS =Saccharomyces cerevisiae GN = TIF31 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DANTGEEVTEDFVNDINV X 0.5813 0.0468 0.1058 0.8113 3.64E+05 K HitAccession Score Mass L(L + H) SD(geo) # 52 P04807 117 54189 0.7785 1.0042 HXKB_YEAST Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ELMQQIENFEK X 0.7802 0.01438 0.24650.9009 7.27E+05 2 3 GFDIPNIENHDVVPMLQK X 0.7742 0.01687 0.1579 0.8352.97E+05 Hit Accession Score Mass L(L + H) SD(geo) # 53 P43545 115 319980.06161 1 SNZ3_YEAST Probable pyridoxine biosynthesis protein SNZ3 OS =Saccharomyces cerevisiae GN = SNZ3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TKGEAGTGDVSEAVK X 0.06161 0.5232 0.2013 0.789 4.12E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 54 P17536 115 23527 0.3192 1TPM1_YEAST Tropomyosin-1 OS = Saccharomyces cerevisiae GN = TPM1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 KNQQLEEDLEESDTK X 0.3192 0.16040.08858 0.7363 1.43E+04 Hit Accession Score Mass L(L + H) SD(geo) # 55P07264 112 85741 0 LEUC_YEAST 3-isopropylmalate dehydratase OS =Saccharomyces cerevisiae GN = LEU1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EFEYKDQDQSSPK 0.302 0.09083 0.02215 0.6239 1.86E+05 2 3DDQGKDQETDFVLNVEP 0.5589 0.01861 0.2447 0.6753 2.83E+06 WR 3 2DDQGKDQETDFVLNVEP 0.8426 0.002 0.7265 0.4088 5.60E+05 WR Hit AccessionScore Mass L(L + H) SD(geo) # 56 P05744 110 12219 0.6213 1RL33A_YEAST 60S ribosomal protein L33-A OS =Saccharomyces cerevisiae GN = RPL33A PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IEGVATPQDAQFYLGK X 0.6213 0.0083 0.1734 0.995 1.38E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 57 P36008 110 46491 0.8109 1EF1G2_YEAST Elongation factor 1-gamma 2 OS =Saccharomyces cerevisiae GN = TEF4 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GQDFAPAFDVAPDWESY X 0.8109 0.01799 0.3455 0.9756 2.24E+05 EYTK HitAccession Score Mass L(L + H) SD(geo) # 58 P16862 108 104953 0.82941.029 2 K6PF2_YEAST 6-phosphofructokinase subunit beta OS =Saccharomyces cerevisiae GN = PFK2 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SSPDENSTLLSNDSISLK X 0.8127 0.01294 0.187 0.9353 1.95E+05 2 3AAEENFNADDKTISDTAA X 0.8594 0.01841 0.2622 0.9073 1.12E+05 VVGVK HitAccession Score Mass L(L + H) SD(geo) # 59 P11154 107 130539 0.9707 1PYC1_YEAST Pyruvate carboxylase 1 OS = Saccharomyces cerevisiae GN =PYC1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 SFLSPLETDEEIEVVIEQG X 0.9707 0.001580.4859 0.886 1.52E+06 K 2 3 EVFVSDGENVDSSDLLVL 0.5025 0.07115 0.13910.5886 1.13E+05 LEDQVPVETK Hit Accession Score Mass L(L + H) SD(geo) #60 P52910 106 75765 0 ACS2_YEAST Acetyl-coenzyme A synthetase 2 OS =Saccharomyces cerevisiae GN = ACS2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TGTEGIPMK 0.6962 0.01855 0.4457 0.1173 7.72E+06 Hit Accession Score MassL(L + H) SD(geo) # 61 P35844 106 49461 0.7224 1KES1_YEAST Protein KES1 OS = Saccharomyces cerevisiae GN = KES1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 NAPSGTLVGDKEDR X 0.7224 0.066230.06821 0.8339 1.10E+05 2 3 DFDYSVTPEEGALVPEKD 0.6484 0.09516 0.2830.6012 1.42E+05 DTFLK Hit Accession Score Mass L(L + H) SD(geo) # 62P36010 105 17268 0 NDK_YEAST Nucleoside diphosphate kinase OS =Saccharomyces cerevisiae GN = YNK1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TFIAVKPDGVQR 0.03719 0.7149 0.1927 0.2162 1.95E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 63 P04802 104 63861 0.8286 1SYDC_YEAST Aspartyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = DPS1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EIGDFEDLSTENEK X 0.8286 0.00835 0.2225 0.9736 4.26E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 64 P12709 104 61582 0.7709 1.002 2G6PI_YEAST Glucose-6-phosphate isomerase OS =Saccharomyces cerevisiae GN = PGI1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3ANKPMYVDGVNVAPEVD X 0.7705 0.01145 0.2097 0.7988 5.44E+05 SVLK 2 2ANKPMYVDGVNVAPEVD X 0.7726 0.02338 0.1041 0.9243 1.51E+05 SVLK HitAccession Score Mass L(L + H) SD(geo) # 65 P15019 104 37302 0.8418 1.4462 TAL1_YEAST Transaldolase OS = Saccharomyces cerevisiae GN = TAL1 PE =1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 DYKGEADPGVISVK X 0.9932 0.011660.08304 0.9874 3.01E+05 2 2 NLAGVDYLTISPALLDK X 0.5131 0.1041 0.1210.9331 6.69E+04 Hit Accession Score Mass L(L + H) SD(geo) # 66 P14120103 11504 0.6528 1 RL30_YEAST 60S ribosomal protein L30 OS =Saccharomyces cerevisiae GN = RPL30 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VYYFQGGNNELGTAVGK X 0.6528 0.01167 0.1559 0.9767 1.26E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 67 P22943 102 11806 0HSP12_YEAST 12 kDa heat shock protein OS = Saccharomyces cerevisiae GN =HSP12 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 68 P0C217 101 199542 0.8624 1.013 2YL14B_YEAST Transposon Ty1-LR4 Gag-Pol polyprotein OS =Saccharomyces cerevisiae GN = TY1B-LR4 PE = 3 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DILSVDYTDIMK X 0.8498 0.02246 0.04882 0.8124 1.27E+05 2 2EVHTNQDPLDVSASK X 0.8722 0.01118 0.2043 0.9837 1.65E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 69 P0C215 101 198422 0.8624 1.013 2YL12B_YEAST Transposon Ty1-LR2 Gag-Pol polyprotein OS =Saccharomyces cerevisiae GN = TY1B-LR2 PE = 3 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DILSVDYTDIMK X 0.8498 0.02246 0.04882 0.8124 1.27E+05 2 2EVHTNQDPLDVSASK X 0.8722 0.01118 0.2043 0.9837 1.65E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 70 P32598 101 35884 0.8363 1PP12_YEAST Serine/threonine-protein phosphatase PP1-2 OS =Saccharomyces cerevisiae GN = GLC7 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GSKPGQQVDLEENEIR X 0.8363 0.01279 0.1472 0.9874 4.79E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 71 P25087 99 43403 0.8036 1ERG6_YEAST Sterol 24-C-methyltransferase OS =Saccharomyces cerevisiae GN = ERG6 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KPENAETPSQTSQEATQ X 0.8036 0.04785 0.08929 0.8981 4.04E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 72 P08524 98 40458 0FPPS_YEAST Farnesyl pyrophosphate synthase OS =Saccharomyces cerevisiae GN = FPP1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IEQLYHEYEESIAK 0.3329 0.09842 0.4172 0.2092 1.03E+06 Hit Accession ScoreMass L(L + H) SD(geo) # 73 P15705 97 66224 0STI1_YEAST Heat shock protein ST11 OS = Saccharomyces cerevisiae GN =STI1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 74 P25694 97 92331 0.8407 1CDC48_YEAST Cell division control protein 48 OS =Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NAPAIIFIDEIDSIAPK X 0.8407 0.0034 0.1098 0.9968 8.16E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 75 P00942 96 26947 0.9321 1TPIS_YEAST Triosephosphate isomerase OS = Saccharomyces cerevisiae GN =TPI1 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ASGAFTGENSVDQIK X 0.9321 0.005790.6559 0.9989 1.71E+06 Hit Accession Score Mass L(L + H) SD(geo) # 76P02400 95 11099 0 RLA4_YEAST 60S acidic ribosomal protein P2-beta OS =Saccharomyces cerevisiae GN = RPP2B PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 77 P40069 94 122525 0IMB4_YEAST Importin subunit beta-4 OS = Saccharomyces cerevisiae GN =KAP123 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations Hit Accession Score Mass L(L + H)SD(geo) # 78 P32481 93 57829 0.8691 1.017 2IF2G_YEAST Eukaryotic translation initiation factor 2 subunit gamma OS =Saccharomyces  cerevisiae GN = GCD11 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LGDEIEIRPGIVTK 0.9246 0.04186 0.2121 0.3448 9.63E+04 2 3VAFTGLEEDGETEEEKR X 0.888 0.00751 0.1402 0.8705 2.90E+05 3 2EFEEGGGLPEQPLNPDF X 0.8595 0.00652 0.4126 0.9885 5.61E+05 SK HitAccession Score Mass L(L + H) SD(geo) # 79 Q12230 92 38048 0.8619 1LSP1_YEAST Sphingolipid long chain base-responsive protein LSP1 OS =Saccharomyces  cerevisiae GN = LSP1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2APTAAELQAPPPPPSSTK X 0.8619 0.03102 0.1585 0.8149 4.28E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 80 P0C0W9 90 19707 0RL11A_YEAST 60S ribosomal protein L11-A OS =Saccharomyces cerevisiae GN = RPL11A PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2VLEQLSGQTPVQSK 0.007131 0.04219 0.7402 0.3062 5.33E+06 Hit AccessionScore Mass L(L + H) SD(geo) # 81 P38788 86 58515 0SSZ1_YEAST Ribosome-associated complex subunit SSZ1 OS =Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 82 P41811 85 99383 0COPB2_YEAST Coatomer subunit beta OS = Saccharomyces cerevisiae GN =SEC27 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 GEIEEAIENVLPNVEGK 0.473 0.09943 0.1130.5911 1.71E+05 Hit Accession Score Mass L(L + H) SD(geo) # 83 P38707 8562168 0 SYNC_YEAST Asparaginyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = DED81 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SVQYVLEDPIAGPLVK 0.5764 0.02059 0.2109 0.4796 4.80E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 84 P00899 85 56732 0TRPE_YEAST Anthranilate synthase component 1 OS =Saccharomyces cerevisiae GN = TRP2 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ESFLLESAK 0.9519 0.00995 0.2493 0.2379 2.91E+05 Hit Accession Score MassL(L + H) SD(geo) # 85 P0C2H6 83 15522 0.6874 1RL27A_YEAST 60S ribosomal protein L27-A OS =Saccharomyces cerevisiae GN = RPL27A PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NQWFFSK 0.618 0.04071 0.1012 0.5142 1.00E+05 2 2 YTLDVEAFK X 0.68740.04111 0.01567 0.7996 2.90E+05 Hit Accession Score Mass L(L + H)SD(geo) # 86 P26321 83 33890 0 RL5_YEAST 60S ribosomal protein L5 OS =Saccharomyces cerevisiae GN = RPL5 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 87 P38115 83 38859 0.118 1ARA1_YEAST D-arabinose dehydrogenase [NAD(P)+] heavy chain OS =Saccharomyces  cerevisiae GN = ARA1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TMYAADGDYLETYK X 0.118 0.1798 0.2653 0.8455 1.50E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 88 P32599 82 72057 0 FIMB_YEAST Fimbrin OS =Saccharomyces cerevisiae GN = SAC6 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 89 A6ZXP4 81 50248 0.3547 1SUB2_YEAS7 ATP-dependent RNA helicase SUB2 OS =Saccharomyces cerevisiae (strain YJM789) GN = SUB2 PE = 3 SV = 1 Modifi-z Sequence Incl. L(L + H) Std. Err. Fraction Correlation Intensitycations 1 2 FLQNPLEIFVDDEAK X 0.3547 0.08683 0.2049 0.8314 2.82E+04 HitAccession Score Mass L(L + H) SD(geo) # 90 P28273 80 140340 0YKV5_YEAST Uncharacterized protein YKL215C OS = Saccharomyces cerevisiaeGN = YKL215C PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations Hit Accession Score Mass L(L + H)SD(geo) # 91 P15625 80 57804 0.7091 1SYFA_YEAST Phenylalanyl-tRNA synthetase alpha chain OS =Saccharomyces cerevisiae GN = FRS2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3DLQDTFYIKDPLTADLPD X 0.7091 0.04609 0.1531 0.7641 1.01E+05 DK HitAccession Score Mass L(L + H) SD(geo) # 92 P38934 80 54606 0.2713 1BFR1_YEAST Nuclear segregation protein BFR1 OS =Saccharomyces cerevisiae GN = BFR1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3INEIEESIASGDLSLVQE X 0.2713 0.04844 0.1734 0.8316 7.51E+05 K HitAccession Score Mass L(L + H) SD(geo) # 93 P05317 78 33866 0.9997 1RLA0_YEAST 60S acidic ribosomal protein P0 OS =Saccharomyces cerevisiae GN = RPP0 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GTIEIVSDVK X 0.9997 0 0.5768 0.9991 4.62E+06 Hit Accession Score MassL(L + H) SD(geo) # 94 P07257 78 40702 0QCR2_YEAST Cytochrome b-c1 complex subunit 2, mitochondrial OS =Saccharomyces  cerevisiae GN = QCR2 PE = 1 SV = 1  Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 95 P46367 77 56688 0.916 1ALDH4_YEAST Potassium-activated aldehyde dehydrogenase, mitochondrialOS = Saccharomyces cerevisiae GN = ALD4 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IAPALVTGNTVVLK X 0.916 0.00158 0.04226 0.9968 5.28E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 96 P16140 77 57713 0.5186 1VATB_YEAST V-type proton ATPase subunit B OS =Saccharomyces cerevisiae GN = VMA2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2AIVQVFEGTSGIDVK X 0.5186 0.06922 0.03856 0.8934 1.27E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 97 P39708 74 49596 0.9962 1DHE5_YEAST NADP-specific glutamate dehydrogenase 2 OS =Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3HIGKDTDVPAGDIGVGG X 0.9962 0.0039 0.09871 0.9621 8.21E+05 R HitAccession Score Mass L(L + H) SD(geo) # 98 P15992 74 23865 0HSP26_YEAST Heat shock protein 26 OS = Saccharomyces cerevisiae GN =HSP26 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 VITLPDYPGVDADNIK 0.1164 0.2258 0.2950.3292 2.05E+05 Hit Accession Score Mass L(L + H) SD(geo) # 99 B3LP78 7355768 0 BLH1_YEAS1 Cysteine proteinase 1, mitochondrial OS =Saccharomyces cerevisiae (strain RM11-1a) GN = LAP3 PE = 3 SV = 2Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations Hit Accession Score Mass L(L + H) SD(geo) # 100 P3232773 130638 0.6239 3.892 2 PYC2_YEAST Pyruvate carboxylase 2 OS =Saccharomyces cerevisiae GN = PYC2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2NFLAPAEPDEEIEVTIEQ X 0.894 0.01442 0.2074 0.9142 9.25E+05 GK 2 3DGESVDASDLLVVLEEE X 0.09446 0.1607 0.3531 0.8345 1.76E+05 TLPPSQK HitAccession Score Mass L(L + H) SD(geo) # 101 P37291 73 52186 0GLYC_YEAST Serine hydroxymethyltransferase, cytosolic OS =Saccharomyces cerevisiae GN = SHM2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LITSHLVDTDPEVDSIIKD 0.6945 0.07766 0.1892 0.388 1.35E+05 EIER HitAccession Score Mass L(L + H) SD(geo) # 102 P60010 73 41663 0.8046 1ACT_YEAST Actin OS = Saccharomyces cerevisiae GN = ACT1 PE = 1 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 3 QEYDESGPSIVHHK 0.674 0.07934 0.1333 0.58766.38E+04 2 2 QEYDESGPSIVHHK X 0.8046 0.02603 0.1087 0.8907 1.96E+05 HitAccession Score Mass L(L + H) SD(geo) # 103 P32582 72 56396 0CBS_YEAST Cystathionine beta-synthase OS = Saccharomyces cerevisiae GN =CYS4 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 104 P01095 71 8585 0 IPB2_YEAST Protease B inhibitors 2 and 1 OS =Saccharomyces cerevisiae GN = PBI2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3HNDVIENVEEDKEVHTN 0.7575 0.01705 0.129 0.6437 5.58E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 105 Q00955 71 250197 0.8507 1ACAC_YEAST Acetyl-CoA carboxylase OS = Saccharomyces cerevisiae GN =FAS3 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 QLSDGGLLIAIGGK X 0.8507 0.017020.06509 0.973 1.45E+05 Hit Accession Score Mass L(L + H) SD(geo) # 106P22203 70 26455 0 VATE_YEAST V-type proton ATPase subunit E OS =Saccharomyces cerevisiae GN = VMA4 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EQSLDGIFEETK 0.3294 0.1126 0.06772 0.6913 3.41E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 107 P38249 70 110276 0.9265 1ElF3A_YEAST Eukaryotic translation initiation factor 3 subunit A OS =Saccharomyces  cerevisiae GN = TIF32 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TAGGSSPATPATPATPA X 0.9265 0.00916 0.2441 0.9925 7.88E+04 TPTPSSGPK HitAccession Score Mass L(L + H) SD(geo) # 108 P09435 69 70504 0HSP73_YEAST Heat shock protein SSA3 OS = Saccharomyces cerevisiae GN =SSA3 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 109 P32588 69 50758 0PUB1_YEAST Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1OS = Saccharomyces cerevisiae GN = PUB1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2QYFQVGGPIANIK 0.9947 0.002 0.3581 0.3382 2.32E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 110 P53900 68 15171 0.05129 1PFD4_YEAST Prefoldin subunit 4 OS = Saccharomyces cerevisiae GN =GIM3 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 NNTQVTFEDQQK X 0.05129 0.3627 0.090040.7859 1.49E+05 Hit Accession Score Mass L(L + H) SD(geo) # 111 P4082568 107940 0 SYAC_YEAST Alanyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = ALA1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TFFETNENAPYLVK 0.9828 0.00532 0.346 0.5419 8.94E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 112 P38631 68 214712 0FKS1_YEAST 1,3-beta-glucan synthase component FKS1 OS =Saccharomyces cerevisiae GN = FKS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3ILAEETAAYEGNENEAE 0.01026 1.465 0.2542 0.6992 1.23E+05 KEDALK HitAccession Score Mass L(L + H) SD(geo) # 113 P47079 67 61952 0TCPQ_YEAST T-complex protein 1 subunit theta OS =Saccharomyces cerevisiae GN = CCT8 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 114 P38205 66 78319 0NCL1_YEAST tRNA (cytosine 5)-methyltransferase NCL1 OS =Saccharomyces cerevisiae GN = NCL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LSSETPALESEGPQTK 0.5913 0.04967 0.1079 0.3943 3.39E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 115 P39939 65 13438 0R526B_YEAST 40S ribosomal protein S26-B OS =Saccharomyces cerevisiae GN = RPS26B PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DLSEASVYPEYALPK 0.3176 0.05414 0.1397 0.3309 6.58E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 116 P35189 64 27423 0.8078 1TAF14_YEAST Transcription initiation factor TFIID subunit 14 OS =Saccharomyces cerevisiae GN = TAF14 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SGSTEETTANTGTIGK X 0.8078 0.02101 0.0963 0.9487 1.58E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 117 Q08972 64 134247 0 NEW1_YEAST [NU+]prion formation protein 1 OS = Saccharomyces cerevisiae GN = NEW1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 ASNLAKPSVDDDDSPAN 0.3162 0.05206 0.1430.3829 2.23E+05 IK Hit Accession Score Mass L(L + H) SD(geo) # 118P05736 63 27392 0.622 1.054 2 RL2_YEAST 60S ribosomal protein L2 OS =Saccharomyces cerevisiae GN = RPL2A PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KVISSDAR X 0.5777 0.00446 0.06036 0.9809 2.68E+04 2 3 ASLNVGNVLPLGSVPEGX 0.624 0.00764 0.308 0.9797 6.09E+05 TIVSNVEEKPGDR Hit Accession ScoreMass L(L + H) SD(geo) # 119 P06367 61 14600 0RS14A_YEAST 40S ribosomal protein S14-A OS =Saccharomyces cerevisiae GN = RPS14A PE = 1 SV = 5 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 120 Q03195 60 68297 0.3246 1RLI1_YEAST Translation initiation factor RLI1 OS =Saccharomyces cerevisiae GN = RLI1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2FDDPPEWQEIIK X 0.3246 0.05303 0.04664 0.8258 2.37E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 121 P23638 60 28697 0PSA4_YEAST Proteasome component Y13 OS = Saccharomyces cerevisiae GN =PRE9 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 122 P33327 60 124254 0.9911 1.026 2DHE2_YEAST NAD-specific glutamate dehydrogenase OS =Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GDIESISDK X 1.001 0.00158 0.3693 0.9924 5.15E+05 2 2 LVSFWAPESELK X0.957 0.01189 0.05111 0.9876 1.49E+05 3 3 RNDTTLLEIVENLK 0.1906 0.24540.2091 0.5903 2.89E+04 Hit Accession Score Mass L(L + H) SD(geo) # 123P17076 59 28107 0.7946 1 RL8A_YEAST 60S ribosomal protein L8-A OS =Saccharomyces cerevisiae GN = RPL8A PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YRPETAAEK X 0.7946 0.00569 0.2624 0.987 1.02E+05 2 3 SKQDASPKPYAVK0.000859 3.397 0.2839 0.2521 2.27E+05 Hit Accession Score Mass L(L + H)SD(geo) # 124 P00815 58 87666 0HIS2_YEAST Histidine biosynthesis trifunctional protein OS =Saccharomyces cerevisiae GN = HIS4 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IKEEAEELTEAK 0.1694 0.3439 0.09508 0.2327 1.01E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 125 P02309 57 11361 0 H4_YEAST Histone H4 OS =Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2DSVTYTEHAK 0.3491 0.08223 0.2286 0.1483 5.70E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 126 P37299 57 8587 0.04592 1QCR10_YEAST Cytochrome b-c1 complex subunit 10 OS =Saccharomyces cerevisiae GN = QCR10 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3IPLLGPTLEDHTPPEDKP X 0.04592 0.3578 0.08934 0.7487 1.68E+05 N HitAccession Score Mass L(L + H) SD(geo) # 127 P23287 55 63355 1 1PP2B1_YEAST Serine/threonine-protein phosphatase 2B catalytic subunit A1OS = Saccharomyces cerevisiae GN = CNA1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3ILNMSTVALSKEPNLLKL X 1 0.001 0.05272 0.9692 2.68E+05 K Hit AccessionScore Mass L(L + H) SD(geo) # 128 P38011 54 34784 0.7242 1GBLP_YEAST Guanine nucleotide-binding protein subunit beta-like proteinOS = Saccharomyces cerevisiae GN = ASC1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3VFSLDPQYLVDDLRPEF X 0.7242 0.00801 0.4127 0.9795 8.90E+05 AGYSK HitAccession Score Mass L(L + H) SD(geo) # 129 P53200 54 28564 0.5579 1AML1_YEAST N(6) adenine-specific DNA methyltransferase-like 1 OS =Saccharomyces  cerevisiae GN = AML1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2EEQQHQEAFQK X 0.5579 0.1156 0.04329 0.7172 6.21E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 130 P32190 52 80158 0GLPK_YEAST Glycerol kinase OS = Saccharomyces cerevisiae GN = GUT1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 131 P19358 51 42470 0.9999 1METK2_YEAST S-adenosylmethionine synthase 2 OS =Saccharomyces cerevisiae GN = SAM2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3TQLQKDIVEK X 0.9999 0.00317 0.04256 0.7785 2.46E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 132 Q12363 50 48353 0.7508 1WTMl_YEAST Transcriptional modulator WTM1 OS =Saccharomyces cerevisiae GN = WTM1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YNPDDTIAPPQDATEES X 0.7508 0.002 0.7573 0.9978 2.44E+05 QTK HitAccession Score Mass L(L + H) SD(geo) # 133 P31539 47 102533 0.8569 1H5104_YEAST Heat shock protein 104 OS = Saccharomyces cerevisiae GN =HSP104 PE = 1 SV = 2 Modifi- z Sequence Incl. L(L + H Std. Err. FractionCorrelation Intensity cations 1 2 GADTNTPLEYLSK X 0.8569 0.01624 0.27230.9822 3.21E+05 Hit Accession Score Mass L(L + H) SD(geo) # 134 P3993546 107036 0.815 1IF4F1_YEAST Eukaryotic initiation factor 4F subunit p150 OS =Saccharomyces cerevisiae GN = TIF4631 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3LKETSDSTSTSTPTPTP X 0.815 0.05328 0.1577 0.8433 8.82E+04 STNDSK HitAccession Score Mass L(L + H) SD(geo) # 135 P35732 46 83923 0.9125 1YKF4_YEAST Uncharacterized protein YKL054C OS = Saccharomyces cerevisiaeGN = YKL054C PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 3 EQVKEEEQTAEELEQE X 0.91250.02943 0.623 0.9847 1.75E+05 QDNVAAPEEEVTVVEEK Hit Accession Score MassL(L + H) SD(geo) # 136 P17255 45 119131 0VATA_YEAST V-type proton ATPase catalytic subunit A OS =Saccharomyces cerevisiae GN = TFP1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 137 P02294 45 14229 0.8421 1H2B2_YEAST Histone H2B.2 OS = Saccharomyces cerevisiae GN = HTB2 PE =1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 QTHPDTGISQK X 0.8421 0.00914 0.14630.9218 1.30E+05 Hit Accession Score Mass L(L + H) SD(geo) # 138 P0229345 14244 0.8421 1 H2B1_YEAST Histone H2B.1 OS =Saccharomyces cerevisiae GN = HTB1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2QTHPDTGISQK X 0.8421 0.00914 0.1463 0.9218 1.30E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 139 P05749 43 13789 0RL22A_YEAST 60S ribosomal protein L22-A OS =Saccharomyces cerevisiae GN = RPL22A PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 140 P40204 43 8477 1 1RUXG_YEAST Small nuclear ribonucleoprotein G OS =Saccharomyces cerevisiae GN = SMX2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KVAGILR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L(L + H)SD(geo) # 141 P08518 43 139256 0RPB2_YEAST DNA-directed RNA polymerase 11 subunit RPB2 OS =Saccharomyces cerevisiae GN = RPB2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 142 P05755 43 22421 0RS9B_YEAST 40S ribosomal protein S9-B OS = Saccharomyces cerevisiae GN =RPS9B PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 143 Q01855 43 15992 0 RS15_YEAST 40S ribosomal protein S15 OS =Saccharomyces cerevisiae GN = RPS15 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LLEMSTEDFVK 0.384 0.05738 0.2239 0.6167 5.45E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 144 P26781 42 17898 1 1RS11_YEAST 40S ribosomal protein S11 OS = Saccharomyces cerevisiae GN =RPS11A PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 1 NAGLGFK X 1 0 0.701 0.99982.17E+06 Hit Accession Score Mass L(L + H) SD(geo) # 145 P00950 42 277840 PMG1_YEAST Phosphoglycerate mutase 1 OS =Saccharomyces cerevisiae GN = GPM1 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity ccations HitAccession Score Mass L(L + H) SD(geo) # 146 P32380 41 112692 0.9554 1NUF1_YEAST Protein NUF1 OS = Saccharomyces cerevisiae GN = NUF1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 IIDLQKK 0.9984 0.00413 0.00899 0.64981.06E+04 2 2 IEIENWK X 0.9554 0.01028 0.1168 0.9842 1.57E+05 HitAccession Score Mass L(L + H) SD(geo) # 147 P16120 41 57439 0THRC_YEAST Threonine synthase OS = Saccharomyces cerevisiae GN =THR4 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 LYIAQEEIPDADLKDLIK 0.04854 0.31080.1234 0.3822 1.17E+06 Hit Accession Score Mass L(L + H) SD(geo) # 148P43616 41 52838 0.6185 1 DUG1_YEAST Cys-Gly metallodipeptidase DUG1 OS =Saccharomyces cerevisiae GN = DUG1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ILIDGIDEMVAPLTEK X 0.6185 0.00821 0.1115 0.9559 3.58E+04 Hit AccessionScore Mass L(L + H) SD(geo) # 149 P25294 38 37567 0.5309 1SIS1_YEAST Protein SIS1 OS = Saccharomyces cerevisiae GN = SIS1 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 YHPDKPTGDTEK X 0.5309 0.05698 0.035410.7338 2.13E+05 Hit Accession Score Mass L(L + H) SD(geo) # 150 P0C0T437 12002 0.8113 1 RS25B_YEAST 40S ribosomal protein S25-B OS =Saccharomyces cerevisiae GN = RPS25B PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3AQHAVILDQEK X 0.8113 0.04438 0.03423 0.7174 2.04E+04 2 3 AQHAVILDQEKYDR0.1884 0.06967 0.3797 0.1743 2.54E+06 Hit Accession Score Mass L(L + H)SD(geo) # 151 Q08438 37 73997 0 VHS3_YEAST Protein VHS3 OS =Saccharomyces cerevisiae GN = VHS3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 152 Q05506 36 69890 0SYRC_YEAST Arginyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = YDR341C PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YGNEEALVK 0.1829 0.1367 0.1933 0.1382 3.93E+05 Hit Accession Score MassL(L + H) SD(geo) # 153 P06168 36 44565 0ILV5_YEAST Ketol-acid reductoisomerase, mitochondrial OS =Saccharomyces cerevisiae GN = ILV5 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 154 P38167 36 123534 0.5931 1ECM21_YEAST Protein ECM21 OS = Saccharomyces cerevisiae GN = ECM21 PE =1 SV = 2 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 SRFNNLDK X 0.5931 0.03207 0.031690.8355 1.66E+05 Hit Accession Score Mass L(L + H) SD(geo) # 155 P0407634 52173 0 ARLY_YEAST Argininosuccinate lyase OS =Saccharomyces cerevisiae GN = ARG4 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 156 P61864 33 8552 0.8436 1UBIQ_YEAST Ubiquitin OS = Saccharomyces cerevisiae GN = UBI1 PE = 1 SV =1 Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 IQDKEGIPPDQQR X 0.8436 0.00578 0.2069 0.96791.11E+06 Hit Accession Score Mass L(L + H) SD(geo) # 157 P54839 33 553240 HMCS_YEAST Hydroxymethylglutaryl-CoA synthase OS =Saccharomyces cerevisiae GN = ERG13 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 158 P40482 33 103842 0SEC24_YEAST Protein transport protein SEC24 OS =Saccharomyces cerevisiae GN = SEC24 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 159 P05694 31 85807 0METE_YEAST 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferaseOS = Saccharomyces cerevisiae GN = MET6 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3APEQFDEVVAAIGNK 0.8993 0.03287 0.3114 0.6099 7.32E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 160 P0C0W1 31 14705 0RS22A_YEAST 40S ribosomal protein S22-A OS =Saccharomyces cerevisiae GN = RPS22A PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 161 P06105 30 135689 0SC160_YEAST Protein SCP160 OS = Saccharomyces cerevisiae GN =SCP160 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 3 FQFLIDAEELKEK 0.2574 0.14950.03011 0.4086 8.22E+04 Hit Accession Score Mass L(L + H) SD(geo) # 162P14065 30 35057 0.8654 1 GCY_YEAST Protein GCY OS =Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GYVVLPK X 0.8654 0.0811 0.06444 0.8822 3.00E+04 Hit Accession Score MassL(L + H) SD(geo) # 163 P52490 29 17561 0UBC13_YEAST Ubiquitin-conjugating enzyme E2 13 OS =Saccharomyces cerevisiae GN = UBC13 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 164 P38994 28 89754 0MSS4_YEAST Probable phosphatidylinositol-4-phosphate 5-kinase MSS4 OS =Saccharomyces  cerevisiae GN = M554 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ISAVTATSTTIK 0.000063 7.067 0.305 0.9995 4.66E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 165 P32893 28 63328 0KRE11_YEAST Beta-glucan synthesis-associated protein KRE11 OS =Saccharomyces  cerevisiae GN = KRE11 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2ASEQLTKK 0.3303 0.2361 0.02043 0.1669 9586 Hit Accession Score MassL(L + H) SD(geo) # 166 A6ZPZ1 28 95169 0.999 1YJ00_YEAS7 UPF0508 protein SCY_2952 OS =Saccharomyces cerevisiae (strain YJM789) GN = SCY_2952 PE = 3 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 SIQVPLSPK X 0.999 0.00323 0.07993 0.9881 3.06E+05Hit Accession Score Mass L(L + H) SD(geo) # 167 P15891 28 65536 0ABP1_YEAST Actin-binding protein OS = Saccharomyces cerevisiae GN =ABP1 PE = 1 SV = 4 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 AEAPKPEVPEDEPEGEP 0.2106 0.084720.3799 0.4288 9.13E+05 DVK Hit Accession Score Mass L(L + H) SD(geo) #168 P32074 27 105239 0.8225 1 COPG_YEAST Coatomer subunit gamma OS =Saccharomyces cerevisiae GN = SEC21 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3SETTLDTTPEAESVPEK X 0.8225 0.02368 0.1323 0.7806 1.44E+05 R HitAccession Score Mass L(L + H) SD(geo) # 169 P04801 27 84987 0SYTC_YEAST Threonyl-tRNA synthetase, cytoplasmic OS =Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 170 B3RHV0 27 28726 0.954 1RS3A1_YEAS1 40S ribosomal protein S1-A OS =Saccharomyces cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1Modifi- z Sequence Incl. L(L + H) Std. Err. Fraction CorrelationIntensity cations 1 2 LRVDEVQGK X 0.954 0.00845 0.1571 0.9013 1.03E+06Hit Accession Score Mass L(L + H) SD(geo) # 171 Q01217 27 95307 0ARG56_YEAST Protein ARG5,6, mitochondrial OS =Saccharomyces cerevisiae GN = ARG5,6 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 172 P32861 27 56234 0.7068 1UGPA1_YEAST UTP--glucose-1-phosphate uridylyltransferase OS =Saccharomyces cerevisiae GN = UGP1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YEIISQQPENVSNLSK X 0.7068 0.00158 0.1676 0.9848 2.66E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 173 Q12462 27 26995 0PEX11_YEAST Peroxisomal membrane protein PMP27 OS =Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 174 P53583 27 61628 0.9997 1MPA43_YEAST Protein MPA43 OS = Saccharomyces cerevisiae GN = MPA43 PE =1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ALQKCLQKLNIR X 0.9997 0 0.5408 0.97924.03E+05 Hit Accession Score Mass L(L + H) SD(geo) # 175 P38737 26211316 1 1 ECM29_YEAST Proteasome component ECM29 OS =Saccharomyces cerevisiae GN = ECM29 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LKNLLR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L(L + H)SD(geo) # 176 P40494 26 90976 1 1PRK1_YEAST Actin-regulating kinase PRK1 OS =Saccharomyces cerevisiae GN = PRK1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LKNLIR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L(L + H)SD(geo) # 177 P36048 26 114578 1 1SN114_YEAST 114 kDa U5 small nuclear ribonucleoprotein component OS =Saccharomyces  cerevisiae GN = SNU114 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LKNLLR X 1 0 0.07689 0.9937 4.35E+05 Hit Accession Score Mass L(L + H)SD(geo) # 178 Q01846 26 130637 0.08842 1MDM1_YEAST Structural protein MDM1 OS = Saccharomyces cerevisiae GN =MDM1 PE = 1 SV = 3 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 TKIYIR X 0.08842 0.1027 0.1197 0.98157.92E+04 Hit Accession Score Mass L(L + H) SD(geo) # 179 P04456 26 159240 RL25_YEAST 60S ribosomal protein L25 OS =Saccharomyces cerevisiae GN = RPL25 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 180 Q99186 24 55352 1.007 1AP2M_YEAST AP-2 complex subunit mu OS = Saccharomyces cerevisiae GN =APM4 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 HSGSDFGNK X 1.007 0.00775 0.037150.9671 4599 Hit Accession Score Mass L(L + H) SD(geo) # 181 Q04922 2353135 0.9994 1 MFB1_YEAST Mitochondrial F-box protein MFB1 OS =Saccharomyces cerevisiae GN = MFB1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KDNPRLK X 0.9994 0.00158 0.4699 0.9983 3.45E+06 Hit Accession Score MassL(L + H) SD(geo) # 182 Q03786 23 22353 0GNTK_YEAST Probable gluconokinase OS = Saccharomyces cerevisiae GN =YDR248C PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 2 KYRDLIR 0.000004 1211 0.066170.9937 3.09E+04 Hit Accession Score Mass L(L + H) SD(geo) # 183 P0414723 64304 0PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear OS =Saccharomyces  cerevisiae GN = PAB1 PE = 1 SV = 4 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YQGVNLFVK 0.6493 0.04431 0.1257 0.2785 2.62E+05 Hit Accession Score MassL(L + H) SD(geo) # 184 P13663 23 39519 0DHAS YEAST Aspartate-semialdehyde dehydrogenase OS =Saccharomyces cerevisiae GN = HOM2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IREDPLLDFK 0.18 0.182 0.08109 0.1847 7.16E+04 Hit Accession Score MassL(L + H) SD(geo) # 185 P19097 23 207964 0FAS2_YEAST Fatty acid synthase subunit alpha OS =Saccharomyces cerevisiae GN = FAS2 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 186 P38264 23 21123 0PHO88_YEAST Inorganic phosphate transport protein PHO88 OS =Saccharomyces cerevisiae GN = PHO88 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SALEHNEVK 0.942 0.01455 0.09329 0.575 5.32E+04 Hit Accession Score MassL(L + H) SD(geo) # 187 P33203 23 69023 0.9927 1PRP40_YEAST Pre-mRNA-processing protein PRP40 OS =Saccharomyces cerevisiae GN = PRP40 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2YLSNRSADQLLK X 0.9927 0.00412 0.2098 0.996 4.72E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 188 P32386 22 189043 0YBT1_YEAST ATP-dependent bile acid permease OS =Saccharomyces cerevisiae GN = YBT1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2IFNMILNK 0.004101 0.9579 0.2443 0.5181 1.15E+06 Hit Accession Score MassL(L + H) SD(geo) # 189 P40075 22 26909 0SCS2_YEAST Vesicle-associated membrane protein-associated protein SCS2OS = Saccharomyces cerevisiae GN = SCS2 PE = 1 SV = 3 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3YLISPDVHPAQNQNIQE 0.6453 0.1021 0.2303 0.4558 6.49E+04 NK Hit AccessionScore Mass L(L + H) SD(geo) # 190 Q06685 22 129674 1.008 1VIP1_YEAST Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinaseOS = Saccharomyces cerevisiae GN = VIP1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SSTSHPKPR X 1.008 0.02117 0.06128 0.7799 7778 Hit Accession Score MassL(L + H) SD(geo) # 191 P46962 21 38057 0CTK2_YEAST CTD kinase subunit beta OS = Saccharomyces cerevisiae GN =CTK2 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 192 P13188 21 93075 0.9115 1 SYQ_YEAST Glutaminyl-tRNA synthetase OS =Saccharomyces cerevisiae GN = GLN4 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SDFSENVDDKEFFR X 0.9115 0.00801 0.1843 0.8822 6.60E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 193 Q02208 21 86313 0.9576 1TOF2_YEAST Topoisomerase 1-associated factor 2 OS =Saccharomyces cerevisiae GN = TOF2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2AESKDLDLLR X 0.9576 0.00992 0.5313 0.8332 4.35E+06 Hit Accession ScoreMass L(L + H) SD(geo) # 194 P43544 21 25116 0.9621 1SNO3_YEAST Probable glutamine amidotransferase SNO3 OS =Saccharomyces cerevisiae GN = SNO3 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LDGKDNGGQELIVAAK X 0.9621 0.00918 0.1046 0.9559 1.74E+05 Hit AccessionScore Mass L(L + H) SD(geo) # 195 P53254 21 141262 0UTP22_YEAST U3 small nucleolar RNA-associated protein 22 OS =Saccharomyces cerevisiae GN = UTP22 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2LSERLTLAQYK 0.002931 1.18 0.313 0.9968 1.09E+06 Hit Accession Score MassL(L + H) SD(geo) # 196 Q12507 21 38997 0.9995 1SFG1_YEAST Superficial pseudohyphal growth protein 1 OS =Saccharomyces cerevisiae GN = SFG1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2TSSKNVK X 0.9995 0.00158 0.4979 0.9993 2.25E+06 Hit Accession Score MassL(L + H) SD(geo) # 197 Q06625 20 175551 0GDE_YEAST Glycogen debranching enzyme OS = Saccharomyces cerevisiae GN =GDB1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations Hit Accession Score Mass L(L + H) SD(geo)# 198 P17555 20 57486 0.7116 1CAP_YEAST Adenylyl cyclase-associated protein OS =Saccharomyces cerevisiae GN = SRV2 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SDGGNIYLSK X 0.7116 0.00648 0.07351 0.9734 7.93E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 199 Q012345 20 28402 0IES3_YEAST Ino eighty subunit 3 OS = Saccharomyces cerevisiae GN =IE53 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 3 IDILTKIQENLLEEYQK 0.7775 0.10230.03577 0.4115 952.5 Hit Accession Score Mass L(L + H) SD(geo) # 200P32802 20 75914 0.9962 1TMN1_YEAST Transmembrane 9 superfamily member 1 OS =Saccharomyces cerevisiae GN = EMP70 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2KIYSSIK X 0.9962 0.02516 0.03919 0.9666 1.24E+04 Hit Accession ScoreMass L(L + H) SD(geo) # 201 P53295 20 40980 0.9333 1YG3Y_YEAST Uncharacterized GTP-binding protein YGR173W OS =Saccharomyces  cerevisiae GN = YGR173W PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 3CLYVYNKIDAVSLEEVD X 0.9333 0.01137 0.1522 0.9687 5.58E+05 K HitAccession Score Mass L(L + H) SD(geo) # 202 P53244 20 65724 0.03843 1ART5_YEAST Arrestin-related trafficking adapter 5 OS =Saccharomyces cerevisiae GN = ART5 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2GRLVLFDK X 0.03843 0.07779 0.03009 0.8963 8.52E+05 Hit Accession ScoreMass L(L + H) SD(geo) # 203 P53598 20 35010 0.9917 1SUCA_YEAST Succinyl-CoA ligase [ADP-forming]subunit alpha, mitochondrial OS = Saccharomyces cerevisiae GN =LSC1 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 ESIPYDK X 0.9917 0.001 0.4495 0.98522.95E+06 Hit Accession Score Mass L(L + H) SD(geo) # 204 P48524 19109107.00 0 BUL1_YEAST Ubiquitin ligase-binding protein BUL1 OS =Saccharomyces cerevisiae GN = BUL1 PE = 1 SV = 1 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations 1 2SPSLHSPK 0.5209 0.06221 0.06108 0.3577 1.00E+05 Hit Accession Score MassL(L + H) SD(geo) # 205 P35172 19 89623 0TREB_YEAST Probable trehalase OS = Saccharomyces cerevisiae GN =NTH2 PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err. FractionCorrelation Intensity cations 1 2 RAFRAAIK 0.05024 0.1466 0.00365 0.22011.25E+04 Hit Accession Score Mass L(L + H) SD(geo) # 206 P10963 18 612010 PCKA_YEAST Phosphoenolpyruvate carboxykinase [ATP] OS =Saccharomyces cerevisiae GN = PCK1 PE = 1 SV = 2 Modifi- z SequenceIncl. L(L + H) Std. Err. Fraction Correlation Intensity cations HitAccession Score Mass L(L + H) SD(geo) # 207 P53133 18 30896 0.8643 1YGL7_YEAST Uncharacterized protein YGL117W OS = Saccharomyces cerevisiaeGN = YGL117W PE = 1 SV = 1 Modifi- z Sequence Incl. L(L + H) Std. Err.Fraction Correlation Intensity cations 1 2 TSLKITHRR X 0.8643 0.016040.0279 0.7852 9.11E+04 Hit Accession Score Mass L(L + H) SD(geo) # 208Q07913 17 38310 0NSE1_YEAST Non-structural maintenance of chromosomes element 1 OS =Saccharomyces  cerevisiae GN = NSE1 PE = 1 SV = 1

TABLE 3 Ribosomal proteins used to establish the non-specificallyassociating baseline for ChAP-MS analyses. The percentage light andstandard deviation are listed for each ribosomal protein. Stdev StdevRibosomal Proteins Glucose Glucose Galactose Galactose 40S ribosomalprotein S10-A OS = Saccharomyces cerevisiae GN = RPS10A 48.01% 1.14%65.47% 0.00% PE = 1 SV = 1 40S ribosomal protein S17-A OS =Saccharomyces cerevisiae GN = RPS17A 47.77% 0.00% 70.60% 4.47% PE = 1 SV= 1 40S ribosomal protein S21-A OS = Saccharomyces cerevisiae GN =RPS21A 53.30% 1.79% 56.17% 1.13% PE = 1 SV = 1 60S ribosomal proteinL14-B OS = Saccharomyces cerevisiae GN = RPL14B 52.21% 4.40% 77.37%10.01% PE = 1 SV = 1 60S ribosomal protein L19 OS = Saccharomycescerevisiae GN = RPL19A PE = 1 50.26% 1.25% 71.05% 5.03% SV = 5 60Sribosomal protein L26-A OS = Saccharomyces cerevisiae GN = RPL26A 51.09%0.00% 70.20% 0.00% PE = 1 SV = 3 60S ribosomal protein L3 OS =Saccharomyces cerevisiae GN = RPL3 PE = 1 49.39% 5.09% 66.83% 7.02% SV =4 60S ribosomal protein L30 OS = Saccharomyces cerevisiae GN = RPL30 PE= 1 48.85% 4.03% 62.85% 4.95% SV = 3 40S ribosomal protein S12 OS =Saccharomyces cerevisiae GN = RPS12 PE = 1 50.92% 13.06% 78.21% 1.50% SV= 1 40S ribosomal protein S19-A OS = Saccharomyces cerevisiae GN =RPS19A 49.03% 1.43% 59.47% 1.64% PE = 1 SV = 2 40S ribosomal proteinS26-A OS = Saccharomyces cerevisiae GN = RPS26A 50.63% 2.36% 71.70%4.02% PE = 1 SV = 1 40S ribosomal protein S4 OS = Saccharomycescerevisiae GN = RPS4A PE = 1 44.54% 11.51% 54.31% 4.61% SV = 3 40Sribosomal protein S7-A OS = Saccharomyces cerevisiae GN = RPS7A 51.87%2.38% 75.86% 6.19% PE = 1 SV = 4 40S ribosomal protein S11 OS =Saccharomyces cerevisiae GN = RPS11A 49.48% 3.94% 74.42% 3.71% PE = 1 SV= 3 60S acidic ribosomal protein P0 OS = Saccharomyces cerevisiae GN =RPP0 50.01% 2.91% 62.25% 3.64% PE = 1 SV = 1 60S ribosomal protein L10OS = Saccharomyces cerevisiae GN = RPL10 PE = 1 53.45% 2.89% 63.81%2.66% SV = 1 60S ribosomal protein L12 OS = Saccharomyces cerevisiae GN= RPL12A PE = 1 51.79% 1.15% 66.76% 2.02% SV = 1 60S ribosomal proteinL30 OS = Saccharomyces cerevisiae GN = RPL30 PE = 1 48.85% 4.03% 63.49%4.82% SV = 3 60S ribosomal protein L9-A OS = Saccharomyces cerevisiae GN= RPL9A PE = 1 49.58% 3.07% 58.70% 2.73% SV = 2 40S ribosomal proteinS1-B OS = Saccharomyces cerevisiae (strain YJM789) 47.63% 4.27% 75.33%9.16% GN = RPS1B PE = 3 SV = 1

TABLE 4 Proteins and PTMs specifically associating with GAL1 chromatinisolated from cells cultured in galactose. Proteins and histoneposttranslational modifications listed are greater than two standarddeviations from the non-specific threshold (80.9% Light). % Light StdevProtein Name Glucose Glucose DNA-directed RNA polymerase II 140 kDapolypeptide (EC 2.7.7.6) (B150)- S cerevisiae 100.00% 0.00% HistoneH3K18acK23ac 100.00% 0.00% Histone H2A.1 OS = Saccharomyces cerevisiaeGN = HTA1 PE = 1 SV = 2 97.10% 6.02% NAD-specific glutamatedehydrogenase OS = Saccharomyces cerevisiae GN = GDH2 PE = 1 SV = 196.09% 2.70% Histone H4K5acK8ac 95.89% 0.00% DNA-directed RNA polymeraseII largest subunit (EC 2.7.7.6) (RNA polymerase II subunit 1) (B220) -94.36% 4.99% S cerevisiae Histone H3K9acK14ac 93.62% 0.00% HistoneH4K12acK16ac 90.56% 3.00% Histone H2B.1 OS = Saccharomyces cerevisiae GN= HTB1 PE = 1 SV = 2 89.59% 9.51% Acetyl-CoA carboxylase OS =Saccharomyces cerevisiae GN = FAS3 PE = 1 SV = 2 89.04% 3.39%6-phosphogluconate dehydrogenase, decarboxylating 1 OS = Saccharomycescerevisiae GN = GND1 PE = 1 87.74% 3.05% SV = 1 Probableinosine-5′-monophosphate dehydrogenase IMD3 OS = Saccharomycescerevisiae GN = IMD3 87.19% 14.00% PE = 1 SV = 1 Eukaryotic translationinitiation factor 3 subunit A OS = Saccharomyces cerevisiae GN = TIF32PE = 1 SV = 1 86.97% 7.61% Histone H3K14ac 85.83% 4.48% Histone H3 OS =Saccharomyces cerevisiae GN = HHT1 PE = 1 SV = 2 85.83% 4.48% Zuotin OS= Saccharomyces cerevisiae GN = ZUO1 PE = 1 SV = 1 85.33% 5.43% ProteinGCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1 85.18% 7.02%Histone H4 OS = Saccharomyces cerevisiae GN = HHF1 PE = 1 SV = 2 90.42%8.84% Actin-related protein 2/3 complex subunit 4 OS = Saccharomycescerevisiae GN = ARC19 PE = 1 SV = 2 84.74% 4.60%Translationally-controlled tumor protein homolog OS = Saccharomycescerevisiae GN = TMA19 PE = 1 SV = 1 84.64% 1.50% Suppressor protein STM1OS = Saccharomyces cerevisiae GN = STM1 PE = 1 SV = 3 84.58% 5.36% FACTcomplex subunit SPT16 OS = Saccharomyces cerevisiae GN = SPT16 PE = 1 SV= 1 84.24% 3.60% Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE= 1 SV = 4 84.22% 5.92% Alcohol dehydrogenase 1 OS = Saccharomycescerevisiae GN = ADH1 PE = 1 SV = 4 83.55% 11.23% Pyruvate carboxylase 1OS = Saccharomyces cerevisiae GN = PYC1 PE = 1 SV = 2 82.51% 7.74%Protein GAL3 OS = Saccharomyces cerevisiae GN = GAL3 PE = 1 SV = 281.95% 8.37% Cell division control protein 48 OS = Saccharomycescerevisiae GN = CDC48 PE = 1 SV = 3 80.99% 2.13%

TABLE 5 Proteins and PTMs specifically associating with GAL1 chromatinisolated from cells cultured in glucose. Proteins and histoneposttranslational modifications listed are greater than two standarddeviations from the non-specific threshold (56.18% Light). % Light StdevProtein Name Glucose Glucose Histone H3K36me3 100.00% 0.00%Glucose-6-phosphate isomerase OS = Saccharomyces cerevisiae GN = PGI1 PE= 1 SV = 3 66.33% 12.98% Magnesium-activated aldehyde dehydrogenase,cytosolic OS = Saccharomyces cerevisiae GN = ALD6 58.78% 9.50% PE = 1 SV= 4 Phosphoglycerate mutase 1 OS = Saccharomyces cerevisiae GN = GPM1 PE= 1 SV = 3 58.62% 6.39% Plasma membrane ATPase 1 OS = Saccharomycescerevisiae GN = PMA1 PE = 1 SV = 2 58.47% 6.81% Cystathioninegamma-lyase OS = Saccharomyces cerevisiae GN = CYS3 PE = 1 SV = 2 58.10%3.72% Enolase 1 OS = Saccharomyces cerevisiae GN = ENO1 PE = 1 SV = 257.88% 2.93% Enolase 2 OS = Saccharomyces cerevisiae GN = ENO2 PE = 1 SV= 2 57.40% 2.33% Heat shock protein SSA4 OS = Saccharomyces cerevisiaeGN = SSA4 PE = 1 SV = 3 56.99% 4.82% Cell division control protein 48 OS= Saccharomyces cerevisiae GN = CDC48 PE = 1 SV = 3 56.59% 4.13%Hexokinase-2 OS = Saccharomyces cerevisiae GN = HXK2 PE = 1 SV = 456.50% 3.43% Fatty acid synthase subunit alpha OS = Saccharomycescerevisiae GN = FAS2 PE = 1 SV = 2 56.19% 6.29%

TABLE 6TAL protein DNA-binding specificity. ChIP was performed for the TAL-PrA used in thisstudy and relative genomic binding was measured with qPCR at each sequence listed below.Real time qPCR primers were used to amplify regions containing the indicated sequencesand enrichment of each was measured relative to ACT1. The standard error of threeanalyses is shown. The first listed DNA sequence at GAL1 (highlighted gray) was usedto design the TAL protein. A BLAST search was used to identify the next five closestbinding sites in the S. cerevisiae genome. Mismatches of these five sequencesrelative to the GAL1 sequence are shown in bold. ChIP-qPCR for ClosestTAL-PrA binding Sequence Chromosome Coordinates Gene Locus tagRelative to Actin

ChrII 278829-278846 GAL1 YBR020W, promoter region 6.14 ± 0.28GGGGTAATTAATCATTTT ChrIV 823079-823066 SCC2 YDR180W 0.65 ± 0.06TTATACATTAATCAGCGA ChrXV 18844-18855 ENB1 between YOL159C 1.34 ± 0.13and YOL158C GGGGTAATTAATGTAAAT ChrXIV 614716-614705 IDP3 YNL009W, 0.94 ±0.46 promoter region AAATTAATCAGCGGTGAC ChrIX 88064-88053 REV7 YIL139C0.77 ± 0.27 GGGGTAATTAAAATTTCT ChrXVI 94211-94221 IQG1 YPL242C 0.76 ±0.10

TABLE 7 Significant proteins (>2-fold enriched) identified with GAL1promoter chromatin from cells grown in galactose-containing media. Thetop 10% of proteins that are >15-fold enriched are highlighted in gray.Spectral Spectral Molecular Counts Counts Proteins Weight TAL-PrA Wildtype

PMA1_YEAST 99,621.60 558 0

YH11B_YEAST (+2) 202,825.20 273 0

DED1_YEAS7 (+1) 65,554.50 261 0

TIF31_YEAST 145,171.10 226 0

PYR1_YEAST 245,129.90 1356 3

EF3B_YEAST 115,871.60 220 0

YO11A_YEAST 49,006.10 216 0

RS3A2_YEAS1 (+3) 28,812.90 204 0

RS3A1_YEAS1 (+4) 28,743.80 189 0

YD12A_YEAST 49,187.40 188 0

GAL2_YEAST 63,627.00 183 0

ASSY_YEAST 46,941.00 177 0

PDR5_YEAST 170,444.10 152 0

FKS1_YEAST 214,859.40 151 0

HSP7E_YEAST 70,086.90 150 0

PDC6_YEAST 61,582.40 150 0

BFR1_YEAST 54,641.70 137 0

RL18_YEAST 20,563.70 129 0

RS2_YEAST 27,450.20 126 0

FKS2_YEAST 216,998.10 126 0

6PGD2_YEAST 53,925.30 118 0

HXT7_YEAST 62,736.00 108 0

GAL3_YEAST 58,130.40 107 0

MS116_YEAST 76,272.50 105 0

ATC6_YEAST 135,274.80 98 0

HXT6_YEAST 62,706.00 98 0

IF2P_YEAST 112,271.50 98 0

RPB1_YEAST 191,615.10 96 0

GAS1_YEAST 59,583.20 94 0

EIF3B_YEAS7 88,131.50 93 0

PGM1_YEAST 63,114.70 91 0

TCPG_YEAST 58,814.70 90 0

SPT16_YEAST 118,636.00 88 0

DBP1_YEAS7 (+1) 67,992.10 87 0

ODP2_YEAST 51,819.70 87 0

CLH_YEAST 187,243.20 173 1

RS8_YEAST 22,490.40 86 0

RPB2_YEAST 138,757.20 85 0

GLNA_YEAST 41,767.10 80 0

TOM40_YEAST 42,039.40 79 0

C1TC_YEAST 102,207.30 76 0

FBRL_YEAST 34,465.50 75 0

SC160_YEAST 134,813.70 300 2

SEC23_YEAST 85,387.60 73 0

NOP56_YEAST 56,867.30 73 0

PYRF_YEAST 29,240.40 71 0

HOSC_YEAST 47,100.30 68 0

NDH1_YEAST 62,776.50 67 0

EIF3C_YEAS7 93,225.20 67 0

ZUO1_YEAST 49,021.50 66 0

TPS2_YEAST 102,978.90 63 0

CARP_YEAST 44,501.00 63 0

RRP5_YEAST 193,141.40 63 0

KAPR_YEAST 47,220.30 62 0 Galactokinase OS = Saccharomyces cerevisiae GN= GAL1 PE = 1 SV = 4 GAL1_YEAST 57,945.00 1350 11 Probable2-methylcitrate dehydratase OS = Saccharomyces cerevisiae PRPD_YEAST57,685.70 61 0 GN = PDH1 PE = 1 SV = 1 2-isopropylmalate synthase 2,mitochondrial OS = Saccharomyces LEU9_YEAST 67,201.00 61 0 cerevisiae GN= LEU9 PE = 1 SV =1 NADH-cytochrome b5 reductase 2 OS = Saccharomycescerevisiae MCR1_YEAS7 34,109.10 61 0 (strain YJM789) GN = MCR1 PE = 2 SV= 1 (+1) 6,7-dimethyl-8-ribityllumazine synthase OS = SaccharomycesRIB4_YEAST 18,555.70 60 0 cerevisiae GN = RIB4 PE = 1 SV = 2N-(5′-phosphoribosyl)anthranilate isomerase OS = SaccharomycesTRPF_YEAST 24,144.90 60 0 cerevisiae GN = TRP1 PE = 1 SV = 2 Glutamatesynthase [NADH] OS = Saccharomyces cerevisiae GLT1_YEAST 238,108.30 58 0GN = GLT1 PE = 1 SV = 2 Nuclear localization sequence-binding protein OS= Saccharomyces NSR1_YEAST 44,536.10 55 0 cerevisiae GN = NSR1 PE = 1 SV= 1 V-type proton ATPase subunit a, vacuolar isoform VPH1_YEAST95,533.10 55 0 OS = Saccharomyces cerevisiae GN = VPH1 PE = 1 SV = 34-aminobutyrate aminotransferase OS = Saccharomyces cerevisiaeGATA_YEAST 52,948.60 55 0 GN = UGA1 PE = 1 SV = 2 Dihydroorotatedehydrogenase OS = Saccharomyces cerevisiae PYRD_YEAST 34,802.70 54 0 GN= URA1 PE = 1 SV = 1 Eukaryotic translation initiation factor 2A OS =Saccharomyces EIF2A_YEAST 71,307.10 54 0 cerevisiae GN = YGR054W PE = 1SV = 1 60S ribosomal protein L32 OS = Saccharomyces cerevisiae GN =RPL32 RL32_YEAST 14,771.80 53 0 PE = 1 SV = 1 60S ribosomal proteinL15-A OS = Saccharomyces cerevisiae RL15A_YEAST 24,422.60 105 1 GN =RPL15A PE = 1 SV =3 Mitochondrial import receptor subunit TOM70 OS =Saccharomyces TOM70_YEAS7 70,127.70 51 0 cerevisiae (strain YJM789) GN =TOM70 PE = 3 SV = 1 (+1) Mitochondrial acidic protein MAM33 OS =Saccharomyces cerevisiae MAM33_YEAST 30,132.70 51 0 GN = MAM33 PE = 1 SV= 1 H/ACA ribonucleoprotein complex subunit 4 OS = SaccharomycesCBF5_YEAST 54,706.30 51 0 cerevisiae GN = CBF5 PE = 1 SV = 1 60Sribosomal protein L8-A OS = Saccharomyces cerevisiae RL8A_YEAST28,125.50 201 2 GN = RPL8A PE = 1 SV = 4 Eukaryotic translationinitiation factor 2 subunit alpha IF2A_YEAST 34,718.70 50 0 OS =Saccharomyces cerevisiae GN = SUI2 PE = 1 SV = 1 NADPH--cytochrome P450reductase OS = Saccharomyces cerevisiae NCPR_YEAST 76,744.20 50 0 GN =NCP1 PE = 1 SV = 3 Nucleolar protein 58 OS = Saccharomyces cerevisiae(strain YJM789) NOP58_YEAS7 56,959.80 98 1 GN = NOP58 PE = 3 SV = 1 (+1)60S ribosomal protein L14-B OS = Saccharomyces cerevisiae RL14B_YEAST15,153.20 97 1 GN = RPL14B PE = 1 SV = 1 Pentafunctional AROMpolypeptide OS = Saccharomyces cerevisiae ARO1_YEAST 174,758.00 97 1 GN= ARO1 PE = 1 SV = 1 60S ribosomal protein L8-B OS = Saccharomycescerevisiae RL8B_YEAST 28,112.80 193 2 GN = RPL8B PE = 1 SV = 3GTP-binding protein RHO1 OS = Saccharomyces cerevisiae GN = RHO1RHO1_YEAST 23,152.00 48 0 PE = 1 SV 3 Invertase 2 OS = Saccharomycescerevisiae GN = SUC2 PE = 1 SV = 1 INV2_YEAST 60,641.00 48 0 (+1)Squalene synthase OS = Saccharomyces cerevisiae GN = ERG9 PE = 1FDFT_YEAST 51,722.50 48 0 SV = 2 Eukaryotic translation initiationfactor 3 subunit B OS = Saccharomyces EIF3B_YEAST 88,131.50 95 1cerevisiae GN = PRT1 PE = 1 SV = 1 Cytochrome c iso-2 OS = Saccharomycescerevisiae GN = CYC7 PE = 1 CYC7_YEAST 12,532.80 47 0 SV = 1ATP-dependent permease PDR15 OS = Saccharomyces cerevisiae PDR15_YEAST172,261.80 47 0 GN = PDR15 PE = 1 SV = 1 60S ribosomal protein L28 OS =Saccharomyces cerevisiae GN = RPL28 RL28_YEAST 16,722.90 46 0 PE = 1 SV= 2 Methionyl-tRNA synthetase, cytoplasmic OS = Saccharomyces SYMC_YEAST85,680.90 46 0 cerevisiae GN = MES1 PE = 1 SV = 4 Eukaryotic translationinitiation factor 3 subunit G OS = Saccharomyces EIF3G_YEAST 30,501.6045 0 cerevisiae GN = TIF35 PE = 1 SV = 1 General transcriptionalcorepressor TUP1 OS = Saccharomyces TUP1_YEAST 78,307.20 45 0 cerevisiaeGN = TUP1 PE = 1 SV = 2 Heat shock protein 42 OS = Saccharomycescerevisiae GN = HSP42 HSP42_YEAST 42,817.50 44 0 PE = 1 SV = 1 60Sribosomal protein L15-B OS = Saccharomyces cerevisiae RL15B_YEAST24,422.60 84 1 GN = RPL15B PE = 1 SV = 2 40S ribosomal protein S23 OS =Saccharomyces cerevisiae RS23_YEAST 16,038.30 42 0 GN = RPS23A PE = 1 SV= 1 T-complex protein 1 subunit theta OS = Saccharomyces cerevisiaeTCPQ_YEAST 61,663.60 42 0 GN = CCT9 PE = 1 SV = 1 26S proteaseregulatory subunit 8 homolog OS = Saccharomyces PRS8_YEAST 45,272.60 410 cerevisiae GN = RPT6 PE = 1 SV = 4 SDO1-like protein YHR087W OS =Saccharomyces cerevisiae SDO1L_YEAST 12,009.80 41 0 GN = YHR087W PE = 1SV = 1 Mitochondrial escape protein 2 OS = Saccharomyces cerevisiaeYME2_YEAST 96,692.20 40 0 GN = YME2 PE = 1 SV = 1 Alpha-soluble NSFattachment protein OS = Saccharomyces cerevisiae SEC17_YEAST 32,804.4040 0 GN = SEC17 PE = 1 SV = 4 Protein translocation protein SEC63 OS =Saccharomyces cerevisiae SEC63_YEAST 75,348.10 40 0 GN = SEC63 PE = 1 SV= 2 Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrialPUT2_YEAST 64,437.50 40 0 OS = Saccharomyces cerevisiae GN = PUT2 PE = 1SV = 2 Polyamine N-acetyltransferase 1 OS = Saccharomyces cerevisiaePAA1_YEAST 21,948.70 79 1 GN = PAA1 PE = 1 SV = 1 40S ribosomal proteinS22-B OS = Saccharomyces cerevisiae RS22B_YEAST 14,626.50 79 1 GN =RPS22B PE = 1 SV = 3 Phosphoinositide phosphatase SAC1 OS =Saccharomyces cerevisiae SAC1_YEAST 71,125.90 38 0 GN = SAC1 PE = 1 SV =1 40S ribosomal protein S26-A OS = Saccharomyces cerevisiae RS26A_YEAST13,505.00 38 0 GN = RPS26A PE = 1 SV = 1 26S proteasome regulatorysubunit RPN2 OS = Saccharomyces RPN2_YEAST 104,237.00 76 1 cerevisiae GN= RPN2 PE = 1 SV = 4 Translational activator GCN1 OS = Saccharomycescerevisiae GCN1_YEAST 296,710.20 38 0 GN = GCN1 PE = 1 SV = 1Dolichyl-diphosphooligosaccharide--protein glycosyltransferaseSTT3_YEAST 81,532.90 38 0 subunit STT3 OS = Saccharomyces cerevisiae GN= STT3 PE = 1 SV = 2 1,3-beta-glucanosyltransferase GAS5 OS =Saccharomyces cerevisiae GAS5_YEAST 51,870.70 38 0 GN = GAS5 PE = 1 SV =1 Acyl-CoA-binding protein OS = Saccharomyces cerevisiae GN = ACB1ACBP_YEAST 10,061.80 38 0 PE = 1 SV = 3 Tricalbin-1 OS = Saccharomycescerevisiae GN = TCB1 PE = 1 SV = 1 TCB1_YEAST 133,581.30 37 0NADP-specific glutamate dehydrogenase 2 OS = Saccharomyces DHE5_YEAST49,627.60 37 0 cerevisiae GN = GDH3 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 1 PMT1_YEAST92,678.00 37 0 OS = Saccharomyces cerevisiae GN = PMT1 PE = 1 SV = 1Mitochondrial import inner membrane translocase subunit TIM10TIM10_YEAST 10,304.60 37 0 OS = Saccharomyces cerevisiae GN = MRS11 PE =1 SV = 1 Ornithine carbamoyltransferase OS = Saccharomyces cerevisiaeOTC_YEAST 37,846.40 37 0 GN = ARG3 PE = 1 SV = 1 Putativemagnesium-dependent phosphatase YER134C MGDP1_YEAST 20,442.40 36 0 OS =Saccharomyces cerevisiae GN = YER134C PE = 1 SV = 1 Eukaryotictranslation initiation factor 4B OS = Saccharomyces IF4B_YEAST 48,522.5036 0 cerevisiae GN = TIF3 PE = 1 SV = 1 Mitochondrial escape protein 2OS = Saccharomyces cerevisiae (strain YME2_YEAS7 96,662.30 36 0 YJM789)GN = YME2 PE = 3 SV = 1 Vesicle-associated membrane protein-associatedprotein SCS2 SCS2_YEAST 26,924.80 36 0 OS = Saccharomyces cerevisiae GN= SCS2 PE = 1 SV = 3 Importin beta SMX1 OS = Saccharomyces cerevisiae GN= SXM1 PE = 1 SXM1_YEAST 108,410.90 36 0 SV = 1 Inorganic phosphatetransport protein PHO88 OS = Saccharomyces PHO88_YEAST 21,138.00 36 0cerevisiae GN = PHO88 PE = 1 SV = 1 Transcription elongation factor SPT6OS = Saccharomyces cerevisiae SPT6_YEAST 168,298.50 71 1 GN = SPT6 PE =1 SV = 1 T-complex protein 1 subunit delta OS = Saccharomyces cerevisiaeTCPD_YEAST 57,605.60 35 0 GN = CCT4 PE = 1 SV = 2 5′-3′ exoribonuclease1 OS = Saccharomyces cerevisiae GN = KEM1 XRN1_YEAST 175,468.00 70 1 PE= 1 SV = 1 Fumarate reductase OS = Saccharomyces cerevisiae GN = YEL047CFRDS_YEAST 50,845.00 35 0 PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 1 HMDH1_YEAST 115,629.1034 0 OS = Saccharomyces cerevisiae GN = HMG1 PE = 1 SV = 1 26Sproteasome regulatory subunit RPN9 OS = Saccharomyces RPN9_YEAST45,785.80 34 0 cerevisiae GN = RPN9 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 2 PMT2_YEAST86,872.80 34 0 OS = Saccharomyces cerevisiae GN = PMT2 PE = 1 SV = 2Bifunctional protein GAL10 OS = Saccharomyces cerevisiae GAL10_YEAST78,197.30 939 14 GN = GAL10 PE = 1 SV = 2 ATP-dependent bile acidpermease OS = Saccharomyces cerevisiae YBT1_YEAST 189,172.20 33 0 GN =YBT1 PE = 1 SV = 2 Saccharopine dehydrogenase [NAD+, L-lysine-forming]LYS1_YEAST 41,466.20 33 0 OS = Saccharomyces cerevisiae GN = LYS1 PE = 1SV = 3 Coatomer subunit gamma OS = Saccharomyces cerevisiae GN = SEC21COPG_YEAST 104,836.20 32 0 PE = 1 SV = 2 Cell division control protein53 OS = Saccharomyces cerevisiae CDC53_YEAST 93,949.60 32 0 GN = CDC53PE = 1 SV = 1 Rotenone-insensitive NADH-ubiquinone oxidoreductase,mitochondrial NDI1_YEAST 57,252.80 32 0 OS = Saccharomyces cerevisiae GN= NDI1 PE = 1 SV = 1 Argininosuccinate lyase OS = Saccharomycescerevisiae GN = ARG4 ARLY_YEAST 51,991.40 32 0 PE = 1 SV = 2 Zinc fingerprotein GIS2 OS = Saccharomyces cerevisiae GN = GIS2 GIS2_YEAST17,102.60 31 0 PE = 1 SV = 1 Protein kinase MCK1 OS = Saccharomycescerevisiae GN = MCK1 MCK1_YEAST 43,137.90 31 0 PE = 1 SV = 1 Malatedehydrogenase, peroxisomal OS = Saccharomyces cerevisiae MDHP_YEAST37,187.20 31 0 GN = MDH3 PE = 1 SV = 3 T-complex protein 1 subunit zetaOS = Saccharomyces cerevisiae TCPZ_YEAST 59,925.90 31 0 GN = CCT6 PE = 1SV = 1 ATP-dependent RNA helicase DBP2 OS = Saccharomyces cerevisiaeDBP2_YEAST 61,001.20 30 0 GN = DBP2 PE = 1 SV = 1 Cytochrome Bpre-mRNA-processing protein 6 OS = Saccharomyces CBP6_YEAST 18,679.70 300 cerevisiae GN = CBP6 PE = 1 SV = 1 Protein DCS2 OS = Saccharomycescerevisiae GN = DCS2 PE = 1 SV = 3 DCS2_YEAST 40,941.80 30 0 Eukaryotictranslation initiation factor 3 subunit A OS = Saccharomyces EIF3A_YEAST110,348.50 176 3 cerevisiae GN = TIF32 PE = 1 SV = 1 Glucose-signalingfactor 2 OS = Saccharomyces cerevisiae GN = GSF2 GSF2_YEAST 45,872.50 581 PE = 1 SV = 1 Glycerol-3-phosphate dehydrogenase [NAD+] 2,mitochondrial GPD2_YEAST 49,422.10 29 0 OS = Saccharomyces cerevisiae GN= GPD2 PE = 1 SV = 2 Prohibitin-2 OS = Saccharomyces cerevisiae GN =PHB2 PE = 1 SV = 2 PHB2_YEAST 34,407.20 29 0 40S ribosomal protein S29-AOS = Saccharomyces cerevisiae RS29A_YEAST 6,660.70 29 0 GN = RPS29A PE =1 SV = 3 DNA-directed RNA polymerase I subunit RPA1 OS = SaccharomycesRPA1_YEAST 186,435.30 29 0 cerevisiae GN = RPA1 PE = 1 SV = 2 Proteintransport protein SEC24 OS = Saccharomyces cerevisiae SEC24_YEAST103,638.70 29 0 GN = SEC24 PE = 1 SV = 1 Carboxypeptidase Y OS =Saccharomyces cerevisiae GN = PRC1 PE = 1 CBPY_YEAST 59,803.60 28 0 SV =1 V-type proton ATPase subunit d OS = Saccharomyces cerevisiaeVA0D_YEAST 39,792.40 28 0 GN = VMA6 PE = 1 SV = 2 Uncharacterizedprotein YJL171C OS = Saccharomyces cerevisiae YJR1_YEAST 43,014.50 28 0GN = YJL171C PE = 1 SV = 1 Vacuolar protein sorting/targeting proteinPEP1 OS = Saccharomyces PEP1_YEAST 177,783.50 28 0 cerevisiae GN = PEP1PE = 1 SV = 1 FACT complex subunit POB3 OS = Saccharomyces cerevisiaePOB3_YEAST 62,995.20 28 0 GN = POB3 PE = 1 SV = 1 Uncharacterizedmitochondrial membrane protein FMP10 FMP10_YEAST 27,698.90 28 0 OS =Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 RNA annealing proteinYRA1 OS = Saccharomyces cerevisiae YRA1_YEAST 24,956.30 27 0 GN = YRA1PE = 1 SV = 2 Mitochondrial outer membrane protein OM45 OS =Saccharomyces OM45_YEAST 44,582.00 27 0 cerevisiae GN = OM45 PE = 1 SV =2 Mitochondrial import receptor subunit TOM5 OS = SaccharomycesTOM5_YEAST 5,987.70 27 0 cerevisiae GN = TOM5 PE = 1 SV = 1 T-complexprotein 1 subunit alpha OS = Saccharomyces cerevisiae TCPA_YEAST60,482.30 27 0 GN = TCP1 PE = 1 SV = 2 Eukaryotic translation initiationfactor 1A OS = Saccharomyces IF1A_YEAST 17,435.70 26 0 cerevisiae GN =TIF11 PE = 1 SV = 1 Protein MSN5 OS = Saccharomyces cerevisiae GN = MSN5PE = 1 SV = 1 MSN5_YEAST 142,126.30 26 0 Putative fatty aldehydedehydrogenase HFD1 OS = Saccharomyces HFD1_YEAST 59,981.90 26 0cerevisiae GN = HFD1 PE = 1 SV = 1 Ergosterol biosynthetic protein 28 OS= Saccharomyces cerevisiae ERG28_YEAST 17,135.80 26 0 GN = ERG28 PE = 1SV = 1 Protein YRO2 OS = Saccharomyces cerevisiae GN = YRO2 PE = 1 SV =1 YRO2_YEAST 38,721.30 26 0 Methylene-fatty-acyl-phospholid synthase OS= Saccharomyces PEM2_YEAST 23,151.10 26 0 cerevisiae GN = PEM2 PE = 1 SV= 1 Protein MKT1 OS = Saccharomyces cerevisiae GN = MKT1 PE = 1 SV = 2MKT1_YEAST 94,499.40 25 0 Protein MRH1 OS = Saccharomyces cerevisiae GN= MRH1 PE = 1 SV = 1 MRH1_YEAST 36,192.40 25 0 Eukaryotic translationinitiation factor 2 subunit beta IF2B_YEAST 31,575.70 25 0 OS =Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2 Peroxiredoxin TSA2 OS =Saccharomyces cerevisiae GN = TSA2 PE = 1 TSA2_YEAST 21,615.40 24 0 SV =3 Endoplasmic reticulum vesicle protein 25 OS = SaccharomycesTMEDA_YEAST 24,106.40 24 0 cerevisiae GN = ERV25 PE = 1 SV = 1 PKHD-typehydroxylase TPA1 OS = Saccharomyces cerevisiae TPA1_YEAST 74,044.60 24 0GN = TPA1 PE = 1 SV = 1 SED5-binding protein 3 OS = Saccharomycescerevisiae GN = SFB3 SFB3_YEAST 103,953.30 24 0 PE = 1 SV = 1 D-lactatedehydrogenase [cytochrome] 3 OS = Saccharomyces DLD3_YEAST 55,226.80 240 cerevisiae GN = DLD3 PE = 1 SV = 1 Single-stranded nucleicacid-binding protein OS = Saccharomyces SSBP1_YEAST 32,989.90 47 1cerevisiae GN = SBP1 PE = 1 SV = 2 Protein CWH43 OS = Saccharomycescerevisiae GN = CWH43 PE = 1 CWH43_YEAST 107,887.70 23 0 SV = 2T-complex protein 1 subunit eta OS = Saccharomyces cerevisiae TCPH_YEAST59,737.10 23 0 GN = CCT7 PE = 1 SV = 1 26S protease regulatory subunit6B homolog OS = Saccharomyces PRS6B_YEAST 47,971.50 23 0 cerevisiae GN =RPT3 PR = 1 SV = 1 NADH-cytochrome b5 reductase 1 OS = Saccharomycescerevisiae NCB5R_YEAST 31,494.80 23 0 GN = CBR1 PE = 1 SV = 2 Glycogendebranching enzyme OS = Saccharomyces cerevisiae GDE_YEAST 174,978.70 461 GN = GDB1 PE = 1 SV = 1 C-5 sterol desaturase OS = Saccharomycescerevisiae GN = ERG3 ERG3_YEAST 42,731.70 23 0 PE = 1 SV = 1 13 kDaribonucleoprotein-associated protein OS = Saccharomyces SNU13_YEAST13,569.40 23 0 cerevisiae GN = SNU13 PE = 1 SV = 1 UPF0202 protein KRE33OS = Saccharomyces cerevisiae GN = KRE33 KRE33_YEAST 119,353.80 23 0 PE= 1 SV = 1 Protein phosphatase PP2A regulatory subunit A OS =Saccharomyces 2AAA_YEAST 70,954.70 23 0 cerevisiae GN = TPD3 PE = 1 SV =2 Eukaryotic translation initiation factor 2 subunit gamma IF2G_YEAST57,867.20 23 0 OS = Saccharomyces cerevisiae GN = GCD11 PE = 1 SV = 1Midasin OS = Saccharomyces cerevisiae GN = MDN1 PE = 1 SV = 1 MDN1_YEAST559,323.50 23 0 Galactose-1-phosphate uridylyltransferase OS =Saccharomyces GAL7_YEAST 42,386.00 459 10 cerevisiae GN = GAL7 PE = 1 SV= 4 UPF0121 membrane protein YLL023C OS = Saccharomyces cerevisiaeYL023_YEAST 32,187.70 22 0 GN = YLL023C PE = 1 SV = 1Phosphatidylinositol transfer protein PDR16 OS = SaccharomycesPDR16_YEAST 40,715.80 22 0 cerevisiae GN = PDR16 PE = 1 SV = 1 60Sribosomal protein L43 OS = Saccharomyces cerevisiae RL43_YEAST 10,090.8022 0 GN = RPL43A PE = 1 SV = 2 Arginine biosynthesis bifunctionalprotein ARG7, mitochondrial ARGJ_YEAST 47,850.20 22 0 OS = Saccharomycescerevisiae GN = ARG7 PE = 1 SV = 1 Probable family 17 glucosidase SCW4OS = Saccharomyces cerevisiae SCW4_YEAST 40,172.20 22 0 GN = SCW4 PE = 1SV = 1 26S protease subunit RPT4 OS = Saccharomyces cerevisiaePRS10_YEAST 49,410.10 22 0 GN = RPT4 PE = 1 SV = 4 60S ribosomal proteinL3 OS = Saccharomyces cerevisiae GN = RPL3 RL3_YEAST 43,757.90 219 5 PE= 1 SV = 4 Phosphoglucomutase-2 OS = Saccharomyces cerevisiae GN = PGM2PGM2_YEAST 63,091.20 345 8 PE = 1 SV = 1 Uncharacterized phosphataseYNL010W OS = Saccharomyces YNB0_YEAST 27,481.40 43 1 cerevisiae GN =YNL010W PE = 1 SV = 1 Elongation factor 3A OS = Saccharomyces cerevisiaeGN = YEF3 PE = 1 EF3A_YEAST 115,996.20 892 21 SV = 3 Casein kinase IIsubunit alpha' OS = Saccharomyces cerevisiae CSK22_YEAST 39,405.00 21 0GN = CKA2 PE = 1 SV = 2 54S ribosomal protein L12, mitochondrial OS =Saccharomyces MNP1_YEAST 20,650.80 21 0 cerevisiae GN = MNP1 PE = 1 SV =1 Nuclear protein SNF4 OS = Saccharomyces cerevisiae GN = SNF4SNF4_YEAST 36,402.50 21 0 PE = 1 SV = 1 Eukaryotic initiation factor 4Fsubunit p150 OS = Saccharomyces IF4F1_YEAST 107,103.80 21 0 cerevisiaeGN = TIF4631 PE = 1 SV = 2 Medium-chain fatty acid ethyl estersynthase/esterase 2 MCFS2_YEAST 51,256.90 21 0 OS = Saccharomycescerevisiae GN = EHT1 PE = 1 SV = 1 ABC transporter ATP-binding proteinARB1 OS = Saccharomyces ARB1_YEAST 68,379.50 21 0 cerevisiae GN = ARB1PE = 1 SV = 1 Cysteinyl-tRNA synthetase OS = Saccharomyces cerevisiaeSYC_YEAST 87,533.90 21 0 GN = YNL247W PE = 1 SV = 1 Protein TTP1 OS =Saccharomyces cerevisiae GN = TTP1 PE = 1 SV = 1 TTP1_YEAST 67,777.60 210 26S proteasome regulatory subunit RPN8 OS = Saccharomyces RPN8_YEAST38,313.90 21 0 cerevisiae GN = RPN8 PE = 1 SV = 3 NADH-cytochrome b5reductase 1 OS = Saccharomyces cerevisiae NCB5R_YEAS7 31,422.60 21 0(strain YJM789) GN = CBR1 PE = 2 SV = 2 ER membrane protein complexsubunit 1 OS = Saccharomyces EMC1_YEAST 87,185.00 21 0 cerevisiae GN =EMC1 PE = 1 SV = 1 Heat shock protein 78, mitochondrial OS =Saccharomyces cerevisiae HSP78_YEAST 91,340.80 292 7 GN = HSP78 PE = 1SV = 2 Nuclear protein STH1/NPS1 OS = Saccharomyces cerevisiaeSTH1_YEAST 156,750.60 20 0 GN = STH1 PE = 1 SV = 1 mRNA-binding proteinPUF3 OS = Saccharomyces cerevisiae PUF3_YEAST 98,070.00 20 0 GN = PUF3PE = 1 SV = 1 Actin-interacting protein 1 OS = Saccharomyces cerevisiaeGN = AIP1 AIP1_YEAST 67,326.00 20 0 PE = 1 SV = 1 Cytochrome c iso-1 OS= Saccharomyces cerevisiae GN = CYC1 PE = 1 CYC1_YEAST 12,182.50 80 2 SV= 2 CTP synthase 1 OS = Saccharomyces cerevisiae GN = URA7 PE = 1URA7_YEAST 64,711.50 20 0 SV = 2 Squalene monooxygenase OS =Saccharomyces cerevisiae GN = ERG1 ERG1_YEAST 55,127.20 20 0 PE = 1 SV =2 Putative aldehyde dehydrogenase-like protein YHR039C MSC7_YEAST71,322.60 20 0 OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1Glucosamine--fructose-6-phosphate aminotransferase [isomerizing]GFA1_YEAST 80,048.70 78 2 OS = Saccharomyces cerevisiae GN = GFA1 PE = 1SV = 4 Uncharacterized GTP-binding protein OLA1 OS = SaccharomycesOLA1_YEAST 44,175.90 155 4 cerevisiae GN = OLA1 PE = 1 SV = 1 Probable1-acyl-sn-glycerol-3-phosphate acyltransferase PLSC_YEAST 33,887.80 19 0OS = Saccharomyces cerevisiae GN = SLC1 PE = 1 SV = 1Sporulation-specific protein 21 OS = Saccharomyces cerevisiaeMPC70_YEAST 69,881.80 19 0 GN = SPO21 PE = 1 SV = 1 Cell divisioncontrol protein 42 OS = Saccharomyces cerevisiae CDC42_YEAST 21,322.6019 0 GN = CDC42 PE = 1 SV = 2 Serine/threonine-protein phosphatase PP-Z2OS = Saccharomyces PPZ2_YEAST 78,494.20 19 0 cerevisiae GN = PPZ2 PE = 1SV = 4 Putative mitochondrial carrier protein YHM1/SHM1 YHM1_YEAST33,217.70 19 0 OS = Saccharomyces cerevisiae GN = YHM1 PE = 1 SV = 1 60Sribosomal protein L24-A OS = Saccharomyces cerevisiae RL24A_YEAST17,614.40 38 1 GN = RPL24A PE = 1 SV = 1 60S ribosomal protein L35 OS =Saccharomyces cerevisiae RL35_YEAST 13,910.20 38 1 GN = RPL35A PE = 1 SV= 1 Mitochondrial respiratory chain complexes assembly protein RCA1RCA1_YEAST 93,280.10 19 0 OS = Saccharomyces cerevisiae GN = RCA1 PE = 1SV = 2 Prohibition-1 OS = Saccharomyces cerevisiae GN = PHB1 PE = 1 SV =2 PHB1_YEAST 31,427.90 38 1 T-complex protein 1 subunit epsilon OS =Saccharomyces cerevisiae TCPE_YEAST 61,916.50 19 0 GN = CCT5 PE = 1 SV =3 Translation machinery-associated protein 22 OS = SaccharomycesDENR_YEAS7 22,495.70 19 0 cerevisiae (strain YJM789) GN = TMA22 PE = 3SV = 1 (+1) DnaJ homolog 1, mitochondrial OS = Saccharomyces cerevisiaeMDJ1_YEAST 55,562.00 19 0 GN = MDJ1 PE = 1 SV = 1Alpha,alpha-trehalose-phosphate synthase [UDP-forming] 56 kDa TPS1_YEAST56,148.30 76 2 subunit OS = Saccharomyces cerevisiae GN = TPS1 PE = 1 SV= 2 Acetyl-coenzyme A synthetase 2 OS = Saccharomyces cerevisiaeACS2_YEAST 75,492.20 228 6 GN = ACS2 PE = 1 SV = 1 60S ribosomal proteinL24-B OS = Saccharomyces cerevisiae RL24B_YEAST 17,548.10 38 1 GN =RPL24B PE = 1 SV = 1 Protein YGP1 OS = Saccharomyces cerevisiae GN =YGP1 PE = 1 SV = 2 YGP1_YEAST 37,328.10 19 0 Actin-related protein 2/3complex subunit 3 OS = Saccharomyces ARPC3_YEAST 20,579.60 19 0cerevisiae GN = ARC18 PE = 1 SV = 1 Isoleucyl-tRNA synthetase,cytoplasmic OS = Saccharomyces SYIC_YEAST 122,988.30 262 7 cerevisiae GN= ILS1 PE = 1 SV = 1 Eukaryotic translation initiation factor 3 subunitI OS = Saccharomyces EIF3I_YEAS7 38,756.20 37 1 cerevisiae (strainYJM789) GN = TIF34 PE = 3 SV = 1 (+1) Dolichol-phosphatemannosyltransferase OS = Saccharomyces DPM1_YEAST 30,363.40 73 2cerevisiae GN = DPM1 PE = 1 SV = 3 40S ribosomal protein S29-B OS =Saccharomyces cerevisiae RS29B_YEAST 6,727.60 18 0 GN = RPS29B PE = 1 SV= 3 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43PRP43_YEAST 87,564.80 18 0 OS = Saccharomyces cerevisiae GN = PRP43 PE =1 SV = 1 Translocation protein SEC72 OS = Saccharomyces cerevisiaeSEC72_YEAST 21,608.40 18 0 GN = SEC72 PE = 1 SV = 3 Transcriptionelongation factor SPT5 OS = Saccharomyces cerevisiae SPT5_YEAST115,651.40 36 1 GN = SPT5 PE = 1 SV = 1 Endoplasmic reticulumtransmembrane protein 1 OS = Saccharomyces YET1_YEAST 23,428.60 18 0cerevisiae GN = YET1 PE = 1 SV = 1 Ferrochelatase, mitochondrial OS =Saccharomyces cerevisiae HEMH_YEAST 44,597.70 18 0 GN = HEM15 PE = 1 SV= 1 Protein CBP3, mitochondrial OS = Saccharomyces cerevisiae CBP3_YEAST39,085.40 18 0 GN = CBP3 PE = 1 SV = 1 Putative proteindisulfide-isomerase YIL005W OS = Saccharomyces YIA5_YEAST 81,223.80 18 0cerevisiae GN = YIL005W PE = 1 SV = 1 Mitochondrial protein importprotein MAS5 OS = Saccharomyces MAS5_YEAST 44,671.70 72 2 cerevisiae GN= YDJ1 PE = 1 SV = 1 Peroxisomal-coenzyme A synthetase OS =Saccharomyces cerevisiae FAT2_YEAST 60,489.90 18 0 GN = FAT2 PE = 1 SV =1 Nuclear cap-binding protein complex subunit 1 OS = SaccharomycesNCBP1_YEAST 100,023.30 36 1 cerevisiae GN = STO1 PE = 1 SV = 2Proteasome component Y13 OS = Saccharomyces cerevisiae PSA4_YEAST28,715.80 18 0 GN = PRE9 PE = 1 SV = 1 Trehalose synthase complexregulatory subunit TSL1 TSL1_YEAST 123,021.70 70 2 OS = Saccharomycescerevisiae GN = TSL1 PE = 1 SV = 1 Ribosomal RNA-processing protein 12OS = Saccharomyces cerevisiae RRP12_YEAST 137,515.10 17 0 GN = RRP12 PE= 1 SV = 1 U3 small nucleolar RNA-associated protein 22 OS =Saccharomyces UTP22_YEAST 140,492.90 17 0 cerevisiae GN = UTP22 PE = 1SV = 1 40S ribosomal protein S26-B OS = Saccharomyces cerevisiaeRS26B_YEAST 13,447.00 34 1 GN = RPS26B PE = 1 SV = 1 Elongator complexprotein 1 OS = Saccharomyces cerevisiae ELP1_YEAST 152,994.20 17 0 GN =IKI3 PE = 1 SV = 1 Probable 1,3-beta-glucanosyltransferase GAS3 OS =Saccharomyces GAS3_YEAST 56,796.00 17 0 cerevisiae GN = GAS3 PE = 1 SV =1 Dynamin-related protein DNM1 OS = Saccharomyces cerevisiae DNM1_YEAST84,976.60 68 2 GN = DNM1 PE = 1 SV = 1 Pyruvate dehydrogenase complexprotein X component, mitochondrial ODPX_YEAST 45,363.80 34 1 OS =Saccharomyces cerevisiae GN = PDX1 PE = 1 SV = 1 GTP-binding proteinRHO3 OS = Saccharomyces cerevisiae GN = RHO3 RHO3_YEAST 25,312.80 17 0PE = 1 SV = 2 DNA-directed RNA polymerase I subunit RPA2 OS =Saccharomyces RPA2_YEAST 135,745.40 33 1 cerevisiae GN = RPA2 PE = 1 SV= 1 54S ribosomal protein YmL6, mitochondrial OS = SaccharomycesRL4P_YEAST 31,970.50 16 0 cerevisiae GN = YML6 PE = 1 SV = 1 ER-derivedvesicles protein ERV29 OS = Saccharomyces cerevisiae ERV29_YEAST35,014.90 16 0 GN = ERV29 PE = 1 SV = 1 54S ribosomal protein L3,mitochondrial OS = Saccharomyces RM03_YEAST 44,001.20 16 0 cerevisiae GN= MRPL3 PE = 1 SV = 2 Pyrroline-5-carboxylate reductase OS =Saccharomyces cerevisiae P5CR_YEAST 30,131.40 16 0 GN = PRO3 PE = 1 SV =1 60S ribosomal protein L34-A OS = Saccharomyces cerevisiae RL34A_YEAST13,639.20 16 0 GN = RPL34A PE = 1 SV = 1 (+1) Serine/threonine-proteinkinase YPK1 OS = Saccharomyces cerevisiae YPK1_YEAST 76,483.80 16 0 GN =YPK1 PE = 1 SV = 2 60S ribosomal protein L19 OS = Saccharomycescerevisiae RL19_YEAST 21,704.60 32 1 GN = RPL19A PE = 1 SV = 5CDP-diacyclglycerol--inositol 3-phosphatidyltransferase PIS_YEAST24,824.30 16 0 OS = Saccharomyces cerevisiae GN = PIS1 PE = 1 SV = 1 60Sribosome subunit biogenesis protein NIP7 OS = Saccharomyces NIP7_YEAST20,381.10 16 0 cerevisiae GN = NIP7 PE = 1 SV = 1 Cell division controlprotein 10 SO = Saccharomyces cerevisiae CDC10_YEAST 37,026.30 16 0 GN =CDC10 PE = 1 SV = 1 E3 ubiquitin-protein ligase RSP5 OS = Saccharomycescerevisiae RSP5_YEAST 91,817.40 16 0 GN = RSP5 PE = 1 SV = 1 Glucan1,3-beta-glucosidase I/II OS = Saccharomyces cerevisiae EXG1_YEAST51,312.30 16 0 GN = EXG1 PE = 1 SV = 1 Eukaryotic translation initiationfactor 5A-2 OS = Saccharomyces IF5A2_YEAST 17,114.60 346 11 cerevisiaeGN = HYP2 PE = 1 SV = 3 1,4-alpha-glucan-branching enzyme OS =Saccharomyces cerevisiae GLGB_YEAST 81,118.50 31 1 GN = GLC3 PE = 1 SV =2 Polyadenylate-binding protein, cytoplasmic and nuclear PABP_YEAST64,345.40 183 6 OS = Saccharomyces cerevisiae GN = PAB1 PE = 1 SV = 4Protein GCY OS = Saccharomyces cerevisiae GN = GCY1 PE = 1 SV = 1GCY_YEAST 35,079.90 272 9 Putative thiosulfate sulfurtransferase YOR285WOS = Saccharomyces YO285_YEAST 15,413.30 30 1 cerevisiae GN = YOR285W PE= 1 SV = 1 DNA topoisomerase 2-associate protein PAT1 OS = SaccharomycesPAT1_YEAST 88,499.40 15 0 cerevisiae GN = PAT1 PE = 1 SV = 3 CAAX prenylprotease 1 OS = Saccharomyces cerevisiae GN = STE24 STE24_YEAST52,327.50 15 0 PE = 1 SV = 1 Endoplasmic reticulum transmembrane protein3 OS = Saccharomyces YET3_YEAST 22,904.20 15 0 cerevisiae GN = YET3 PE =1 SV = 1 ATP-dependent RNA helicase DOB1 OS = Saccharomyces cerevisiaeMTR4_YEAST 122,058.70 15 0 GN = MTR4 PE = 1 SV = 1 Translationmachinery-associated protein 17 OS = Saccharomyces TMA17_YEAST 16,771.9015 0 cerevisiae GN = TMA17 PE = 1 SV = 1 Carbon catabolite-derepressingprotein kinase OS = Saccharomyces SNF1_YEAST 72,047.90 15 0 cerevisiaeGN = SNF1 PE = 1 SV = 1 tRNA (cytosine-5-)-methyltransferase NCL1 OS =Saccharomyces NCL1_YEAST 77,879.60 15 0 cerevisiae GN = NCL1 PE = 1 SV =1 Protein transport protein SEC61 OS = Saccharomyces cerevisiaeSC61A_YEAST 52,940.20 15 0 GN = SEC61 PE = 1 SV = 1 Calcineurin subunitB OS = Saccharomyces cerevisiae GN = CNB1 CANB_YEAST 19,640.10 15 0 PE =1 SV = 3 Lysophospholipase 1 OS = Saccharomyces cerevisiae GN = PLB1 PE= 1 PLB1_YEAST 71,670.00 15 0 SV = 2 Proteasome component Y7 OS =Saccharomyces cerevisiae GN = PRE8 PSA2_YEAST 27,163.10 15 0 PE = 1 SV =1 Metal resistance protein YCF1 OS = Saccharomyces cerevisiae YCFI_YEAST171,129.30 15 0 GN = YCF1 PE = 1 SV = 2 Ran GTPase-activating protein 1OS = Saccharomyces cerevisiae RNA1_YEAST 45,817.80 15 0 GN = RNA1 PE = 1SV = 2 L-aminoadipate-semialdehyde dehydrogenase OS = SaccharomycesLYS2_YEAST 155,350.80 30 1 cerevisiae GN = LYS2 PE = 1 SV = 2 Serinehydroxymethyltransferase, mitochondrial OS = Saccharomyces GLYM_YEAST53,688.00 30 1 cerevisiae GN = SHM1 PE = 1 SV = 2 Coatomer subunit alphaOS = Saccharomyces cerevisiae GN = RET1 COPA_YEAST 135,611.20 89 3 PE =1 SV = 2 40S ribosomal protein S10-B OS = Saccharomyces cerevisiaeRS10B_YEAST 12,738.70 89 3 GN = RPS10B PE = 1 SV = 1 40S ribosomalprotein S10-A OS = Saccharomyces cerevisiae RS10A_YEAST 12,739.70 89 3GN = RPS10A PE = 1 SV = 1 Tryptophan synthase OS = Saccharomycescerevisiae GN = TRP5 PE = 1 TRP_YEAST 76,626.60 59 2 SV = 1Serine/threonine-protein phosphatase PP1-2 OS = Saccharomyces PP12_YEAST35,909.00 58 2 cerevisiae GN = GLC7 PE = 1 SV = 1 Aminopeptidase Y OSSaccharomyces cerevisiae GN = APE3 PE = 1 APE3_YEAST 60,139.20 29 1 SV =1 Glycerol-3-phosphate dehydrogenase [NAD+] 1 OS = SaccharomycesGPD1_YEAST 42,868.60 115 4 cerevisiae GN = GPD1 PE = 1 SV = 4 Valyl-tRNAsynthetase, mitochondrial OS = Saccharomyces cerevisiae SYV_YEAST125,774.70 172 6 GN = VAS1 PE = 1 SV = 2 Aconitate hydratase,mitochondrial OS = Saccharomyces cerevisiae ACON_YEAST 85,371.60 688 24GN = ACO1 PE = 1 SV = 2 Elongation factor Tu, mitochondrial OS =Saccharomyces cerevisiae EFTU_YEAST 47,972.90 57 2 GN = TUF1 PE = 1 SV =1 Glycerol-3-phosphate O-acyltransferase 2 OS = Saccharomyces GPT2_YEAST83,648.60 14 0 cerevisiae GN = GPT2 PE = 1 SV = 1 Putative ribosomal RNAmethyltransferase Nop2 OS = Saccharomyces NOP2_YEAST 69,814.30 14 0cerevisiae GN = NOP2 PE = 1 SV = 1 Serine/threonine-protein kinaseYPK2/YKR2 OS = Saccharomyces YPK2_YEAST 76,669.00 14 0 cerevisiae GN =YPK2 PE = 1 SV = 1 Xanthine phosphoribosyltransferase 1 OS =Saccharomyces cerevisiae XPT1_YEAST 23,672.00 14 0 GN = XPT1 PE = 1 SV =1 3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 HMDH2_YEAST115,696.90 14 0 OS = Saccharomyces cerevisiae GN = HMG2 PE = 1 SV = 13-keto-steroid reductase OS = Saccharomyces cerevisiae GN = ERG27ERG27_YEAST 39,726.60 14 0 PE = 1 SV = 1 Ras-like protein 2 OS =Saccharomyces cerevisiae GN = RAS2 PE = 1 RAS2_YEAST 34,705.00 14 0 SV =4 Protein phosphatase 1 regulatory subunit SDS22 OS = SaccharomycesSDS22_YEAST 38,890.20 14 0 cerevisiae GN = SDS22 PE = 1 SV = 1Ubiquitin-like protein SMT3 OS = Saccharomyces cerevisiae GN = SMT3SMT3_YEAST 11,597.50 28 1 PE = 1 SV = 1 Sphingosine-1-phosphate lyase OS= Saccharomyces cerevisiae SGPL_YEAST 65,567.50 14 0 GN = DPL1 PE = 1 SV= 1 Protein transport protein SSS1 OS = Saccharomyces cerevisiaeSC61G_YEAST 8,943.80 14 0 GN = SSS1 PE = 1 SV = 2 UPF0674 endoplasmicreticulum membrane protein YNR021W YN8B_YEAST 47,095.10 14 0 OS =Saccharomyces cerevisiae GN = YNR021W PE = 1 SV = 3 Non-classical exportprotein 2 OS = Saccharomyces cerevisiae NCE2_YEAST 18,967.70 14 0 GN =NCE102 PE = 1 SV = 1 Reduced viability upon starvation protein 161 OS =Saccharomyces RV161_YEAST 30,251.90 14 0 cerevisiae GN = RVS161 PE = 1SV = 1 Cytochrome b5 OS = Saccharomyces cerevisiae GN = CYB5 PE = 1CYB5_YEAST 13,297.10 14 0 SV = 2 60S ribosomal protein L37-A OS =Saccharomyces cerevisiae RL37A_YEAST 9,850.40 14 0 GN = RPL37A PE = 1 SV= 2 Calmodulin OS = Saccharomyces cerevisiae GN = CMD1 PE = 1 SV = 1CALM_YEAST 16,135.50 14 0 Actin-related protein 2/3 complex subunit 5 OS= Saccharomyces ARPC5_YEAST 17,134.60 14 0 cerevisiae GN = ARC15 PE = 1SV = 1 Mitochondrial outer membrane protein SCY_3392 YKR18_YEAS781,773.40 14 0 OS = Saccharomyces cerevisiae (strain YJM789) GN =SCY_3392 PE = 3 (+1) SV = 1 tRNA pseudouridine synthase 1 OS =Saccharomyces cerevisiae PUS1_YEAST 62,145.30 14 0 GN = PUS1 PE = 1 SV =1 Heterotrimeric G protein gamma subunit GPG1 OS = SaccharomycesGPG1_YEAST 14,922.30 14 0 cerevisiae GN = GPG1 PE = 1 SV = 1Anthranilate synthase component 1 OS = Saccharomyces cerevisiaeTRPE_YEAST 56,769.50 14 0 GN = TRP2 PE = 1 SV = 4 UPF0662 proteinYPL260W OS = Saccharomyces cerevisiae YP260_YEAST 62,782.70 27 1 GN =YPL260W PE = 1 SV = 1 NADPH-dependent 1-acyldihydroxyacetone phosphatereductase AYR1_YEAST 32,815.30 27 1 OS = Saccharomyces cerevisiae GN =AYR1 PE = 1 SV = 1 Long-chain-fatty-acid--CoA ligase 1 OS =Saccharomyces cerevisiae LCF1_YEAST 77,868.10 81 3 GN = FAA1 PE = 1 SV =1 Small COPII coat GTPase SAR1 OS = Saccharomyces cerevisiae SAR1_YEAST21,451.50 53 2 GN = SAR1 PE = 1 SV = 1 GMP synthase[glutamine-hydrolyzing] OS = Saccharomyces cerevisiae GUAA_YEAST58,483.40 53 2 GN = GUA1 PE = 1 SV = 4 Mitochondrial outer membraneprotein porin 1 OS = Saccharomyces VDAC1_YEAST 30,429.50 185 7cerevisiae GN = POR1 PE = 1 SV = 4 ATP-dependent helicase NAM7 OS =Saccharomyces cerevisiae NAM7_YEAST 109,432.60 13 0 GN = NAM7 PE = 1 SV= 1 Proteasome component PRE2 OS = Saccharomyces cerevisiae PSB5_YEAST31,636.90 13 0 GN = PRE2 PE = 1 SV = 3 Homocitrate synthase,mitochondrial OS = Saccharomyces cerevisiae HOSM_YEAST 48,595.50 78 3 GN= LYS21 PE = 1 SV = 1 Nucleolar complex protein 2 OS = Saccharomycescerevisiae NOC2_YEAST 81,605.10 13 0 GN = NOC2 PE = 1 SV = 2Transcriptional regulatory protein SIN3 OS = Saccharomyces cerevisiaeSIN3_YEAST 174,843.10 13 0 GN = SIN3 PE = 1 SV = 2 Ribosome biogenesisprotein ERB1 OS = Saccharomyces cerevisiae ERB1_YEAS7 91,706.30 13 0(strain YJM789) GN = ERB1 PE = 3 SV = 1 (+1) Dihydroxy-acid dehydratase,mitochondrial OS = Saccharomyces ILV3_YEAST 62,862.80 78 3 cerevisiae GN= ILV3 PE = 1 SV = 2 Uncharacterized protein YKL054C OS = Saccharomycescerevisiae YKF4_YEAST 83,968.30 13 0 GN = YKL054C PE = 1 SV = 1DNA-directed RNA polymerases I, II, and III subunit RPABC5 RPAB5_YEAST8,278.00 13 0 OS = Saccharomyces cerevisiae GN = RPB10 PE = 1 SV = 2Mitochondrial presequence protease OS = Saccharomyces cerevisiaeCYM1_YEAST 112,185.50 26 1 GN = CYM1 PE = 1 SV = 2Amidophosphoribosyltransferase OS = Saccharomyces cerevisiae PUR1_YEAST56,720.30 13 0 GN = ADE4 PE = 1 SV = 2 Protein ERP1 OS = Saccharomycescerevisiae GN = ERP1 PE = 1 SV = 1 ERP1_YEAST 24,724.00 13 0 Hsp90co-chaperone HCH1 OS = Saccharomyces cerevisiae HCH1_YEAST 17,246.80 130 GN = HCH1 PE = 1 SV = 1 Acetyl-CoA carboxylase OS = Saccharomycescerevisiae GN = FAS3 ACAC_YEAST 250,359.50 572 22 PE = 1 SV = 2Mitochondrial outer membrane protein IML2 OS = Saccharomyces IML2_YEAS782,553.00 13 0 cerevisiae (strain YJM789) GN = IML2 PE = 3 SV = 1 (+1)Choline-phosphate cytidylyltransferase OS = Saccharomyces cerevisiaePCY1_YEAST 49,408.40 13 0 GN = PCT1 PE = 1 SV = 2 Nucleosome assemblyprotein OS = Saccharomyces cerevisiae NAP1_YEAST 47,886.10 13 0 GN =NAP1 PE = 1 SV =2 THO complex subunit 2 OS = Saccharomyces cerevisiae GN= THO2 THO2_YEAST 183,940.50 13 0 PE = 1 SV = 1 Sec sixty-one proteinhomolog OS = Saccharomyces cerevisiae SSH1_YEAST 53,314.50 13 0 GN =SSH1 PE = 1 SV = 1 Cytochrome c heme lyase OS = Saccharomyces cerevisiaeGN = CYC3 CCHL_YEAST 30,080.70 13 0 PE = 1 SV = 1 Prefoldin subunit 4 OS= Saccharomyces cerevisiae GN = GIM3 PE = 1 PFD4_YEAST 15,181.00 13 0 SV= 1 Gamma-glutamyl phosphate reductase OS = Saccharomyces cerevisiaePROA_YEAST 49,742.20 13 0 GN = PRO2 PE = 1 SV = 1 60S ribosomal proteinL37-B OS = Saccharomyces cerevisiae RL37B_YEAST 9,868.30 13 0 GN =RPL37B PE = 1 SV = 2 UPF0368 protein YPL225W OS = Saccharomycescerevisiae YP225_YEAST 17,445.20 26 1 GN = YPL225W PE = 1 SV = 1Dolichyl-phosphate-mannose--protein mannosyltransferase 4 PMT4_YEAST87,968.60 13 0 OS = Saccharomyces cerevisiae GN = PMT4 PE = 1 SV = 1Increased sodium tolerance protein 2 OS = Saccharomyces cerevisiaeIST2_YEAST 105,908.10 13 0 GN = IST2 PE = 1 SV = 1 Glucokinase-1 OS =Saccharomyces cerevisiae GN = GLK1 PE = 1 SV = 1 HXKG_YEAST 55,379.10231 9 Suppressor protein STM1 OS = Saccharomyces cerevisiae GN = STM1STM1_YEAST 29,995.40 202 8 PE = 1 SV = 3 Uridylate kinase OS =Saccharomyces cerevisiae GN = URA6 PE = 1 UMPK_YEAST 22,933.90 12 0 SV =1 Myosin light chain 1 OS = Saccharomyces cerevisiae GN = MLC1 PE = 1MLC1_YEAST 16,445.30 24 1 SV = 1 Glucose-repressible alcoholdehydrogenase transcriptional effector CCR4_YEAST 94,702.70 12 0 OS =Saccharomyces cerevisiae GN = CCR4 PE = 1 SV = 1 54S ribosomal proteinL1, mitochondrial OS = Saccharomyces cerevisiae RM01_YEAST 30,997.30 120 GN = MRPL1 PE = 1 SV = 1 Nuclear polyadenylated RNA-binding protein 3OS = Saccharomyces NAB3_YEAST 90,438.50 12 0 cerevisiae GN = NAB3 PE = 1SV = 1 Phosphoglycerate mutase 2 OS = Saccharomyces cerevisiaePMG2_YEAST 36,074.50 12 0 GN = GPM2 PE = 1 SV = 1 3′(2′),5′-bisphosphatenucleotidase OS = Saccharomyces cerevisiae HAL2_YEAST 39,150.30 12 0 GN= HAL2 PE = 1 SV = 1 Protein SEY1 OS = Saccharomyces cerevisiae (strainAWRI1631) SEY1_YEAS6 89,425.20 12 0 GN = SEY1 PE = 3 SV = 1 (+2)Thiamine metabolism regulatory protein THI3 OS = SaccharomycesTHI3_YEAST 68,367.90 12 0 cerevisiae GN = THI3 PE = 1 SV = 1Alpha-mannosidase OS = Saccharomyces cerevisiae GN = AMS1 PE = 1MAN1_YEAST 124,503.20 24 1 SV = 2 [NU+] prion formation protein 1 OS =Saccharomyces cerevisiae NEW1_YEAST 134,335.50 12 0 GN = NEW1 PE = 1 SV= 1 T-complex protein 1 subunit beta OS = Saccharomyces cerevisiaeTCPB_YEAST 57,205.70 12 0 GN = CCT2 PE = 1 SV = 1 Putative zincmetalloproteinase YIL108W OS = Saccharomyces cerevisiae YIK8_YEAST77,416.50 12 0 GN = YIL108W PE = 1 SV = 1 Prefoldin subunit 5 OS =Saccharomyces cerevisiae GN = GIM5 PE = 1 PFD5_YEAST 18,356.30 12 0 SV =1 Probable glycosidase CRH2 OS = Saccharomyces cerevisiae CRH2_YEAST49,906.20 12 0 GN = UTR2 PE = 1 SV = 3 Coatomer subunit epsilon OS =Saccharomyces cerevisiae GN = SEC28 COPE_YEAST 33,830.60 12 0 PE = 1 SV= 2 26S proteasome regulatory subunit RPN13 OS = Saccharomycescerevisiae RPN13_YEAST 17,902.50 12 0 GN = RPN13 PE = 1 SV = 1 40Sribosomal protein S28-A OS = Saccharomyces cerevisiae RS28A_YEAST7,591.70 24 1 GN = RPS28A PE = 1 SV = 1 D-3-phosphoglyceratedehydrogenase 1 OS = Saccharomyces cerevisiae SERA_YEAST 51,194.10 12 0GN = SER3 PE = 1 SV = 1 Adenylosuccinate synthetase OS = Saccharomycescerevisiae PURA_YEAST 48,280.40 12 0 GN = ADE12 PE = 1 SV = 3 CTPsynthase 2 OS = Saccharomyces cerevisiae (strain YJM789) URA8_YEAS764,497.40 12 0 GN = URA8 PE = 3 SV = 1 (+1) ATP-dependent RNA helicaseHAS1 OS = Saccharomyces cerevisiae HAS1_YEAST 56,720.20 12 0 GN = HAS1PE = 1 SV = 1 Zinc finger protein ZPR1 OS = Saccharomyces cerevisiae GN= ZPR1 ZPR1_YEAST 55,072.70 12 0 PE = 1 SV = 1 26S proteasome regulatorysubunit RPN3 OS = Saccharomyces cerevisiae RPN3_YEAST 60,426.30 12 0 GN= RPN3 PE = 1 SV = 4 Peroxisomal membrane protein PMP27 OS =Saccharomyces cerevisiae PEX11_YEAST 26,876.20 12 0 GN = PEX11 PE = 1 SV= 2 Ribose-phosphate pyrophosphokinase 5 OS = Saccharomyces cerevisiaeKPR5_YEAST 53,506.20 12 0 GN = PRS5 PE = 1 SV = 1 U6 snRNA-associatedSm-like protein LSm6 OS = Saccharomyces LSM6_YEAS7 9,398.00 12 0cerevisiae (strain YJM789) GN = LSM6 PE = 3 SV = 1 (+1) Protein HMF1 OS= Saccharomyces cerevisiae GN = HMF1 PE = 1 SV = 1 HMF1_YEAST 13,905.9012 0 General negative regulator of transcription subunit 1 NOT1_YEAST240,344.80 12 0 OS = Saccharomyces cerevisiae GN = NOT1 PE = 1 SV = 2Putative glucokinase-2 OS = Saccharomyces cerevisiae GN = EMI2EMI2_YEAST 55,923.00 92 4 PE = 1 SV = 1 26S protease regulatory subunit4 homolog OS = Saccharomyces cerevisiae PRS4_YEAST 48,830.50 23 1 GN =RPT2 PE = 1 SV = 3 Sphingolipid long chain base-responsive protein LSP1LSP1_YEAST 38,071.60 113 5 OS = Saccharomyces cerevisiae GN = LSP1 PE =1 SV = 1 UPF0001 protein YBL036C OS = Saccharomyces cerevisiaeYBD6_YEAST 29,124.20 11 0 GN = YBL036C PE = 1 SV = 1 Galactose/lactosemetabolism regulatory protein GAL80 GAL80_YEAST 48,325.40 11 0 OS =Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2 U3 small nucleolarribonucleoprotein protein IMP3 IMP3_YEAST 21,886.10 11 0 OS =Saccharomyces cerevisiae GN = IMP3 PE = 1 SV = 1 U3 small nucleolarRNA-associated protein 21 OS = Saccharomyces UTP21_YEAST 104,794.60 11 0cerevisiae GN = UTP21 PE = 1 SV = 1 DNA polymerase alpha catalyticsubunit A OS = Saccharomyces DPOA_YEAST 166,815.30 11 0 cerevisiae GN =POL1 PE = 1 SV = 2 Probable glycerophosphodiester phosphodiesteraseYPL206C YP206_YEAST 37,071.30 11 0 OS = Saccharomyces cerevisiae GN =YPL206C PE = 1 SV = 1 Cytochrome c oxidase assembly protein COX15 OS =Saccharomyces COX15_YEAST 54,660.50 11 0 cerevisiae GN = COX15 PE = 1 SV= 1 U6 snRNA-associated Sm-like protein LSm5 OS = SaccharomycesLSM5_YEAST 10,423.20 11 0 cerevisiae GN = LSM5 PE = 1 SV = 1 60Sribosomal protein L29 OS = Saccharomyces cerevisiae GN = RPL29RL29_YEAST 6,669.10 11 0 PE = 1 SV = 3 Tricalbin-3 OS = Saccharomycescerevisiae GN = TCB3 PE = 1 SV = 1 TCB3_YEAST 171,081.40 22 1Peroxiredoxin HYR1 OS = Saccharomyces cerevisiae GN = HYR1 PE = 1GPX3_YEAST 18,642.20 22 1 SV = 1 Glucose-6-phosphate 1-dehydrogenase OS= Saccharomyces cerevisiae G6PD_YEAST 57,523.60 44 2 GN = ZWF1 PE = 1 SV= 4 Endosomal protein P24B OS = Saccharomyces cerevisiae GN = EMP24EMP24_YEAST 23,332.70 11 0 PE = 1 SV = 1 Proteasome component C1 OS =Saccharomyces cerevisiae PSA3_YEAST 31,536.40 11 0 GN = PRE10 PE = 1 SV= 2 26S proteasome regulatory subunit RPN6 OS = Saccharomyces cerevisiaeRPN6_YEAST 49,776.20 11 0 GN = RPN6 PE = 1 SV = 3 Monothiolglutaredoxin-3 OS = Saccharomyces cerevisiae GN = GRX3 GLRX3_YEAST32,481.70 11 0 PE = 1 SV = 1 C-8 sterol isomerase OS = Saccharomycescerevisiae GN = ERG2 PE = 1 ERG2_YEAST 24,896.60 11 0 SV = 1Uncharacterized membrane glycoprotein YNR065C YN94_YEAST 125,204.80 11 0OS = Saccharomyces cerevisiae GN = YNR065C PE = 1 SV = 1 Ubiquitincarboxyl-terminal hydrolase 6 OS = Saccharomyces cerevisiae UBP6_YEAST57,112.50 11 0 GN = UBP6 PE = 1 SV = 1 Histone chaperone ASF1 OS =Saccharomyces cerevisiae GN = ASF1 ASF1_YEAST 31,603.10 11 0 PE = 1 SV =1 Pumilio homology domain family member 6 OS = Saccharomyces PUF6_YEAST75,109.00 22 1 cerevisiae GN = PUF6 PE = 1 SV = 1 Mitochondrial outermembrane protein OM14 OS = Saccharomyces OM14_YEAS7 14,609.90 11 0cerevisiae (strain YJM789) GM = OM14 PE = 3 SV = 1 (+1) AP-1 complexsubunit gamma-1 OS = Saccharomyces cerevisiae AP1G1_YEAST 93,631.50 11 0GN = APL4 PE = 1 SV = 1 Signal recognition particle subunit SRP72 OS =Saccharomyces cerevisiae SRP72_YEAST 73,544.80 11 0 GN = SRP72 PE = 1 SV= 2 Protein transport protein SEC31 OS = Saccharomyces cerevisiaeSEC31_YEAST 138,706.80 11 0 GN = SEC31 PE = 1 SV = 2Phosphatidylethanolamine N-methyltransferase OS = SaccharomycesPEM1_YEAST 101,208.50 11 0 cerevisiae GN = PEM1 PE = 1 SV = 1Mitochondrial import inner membrane translocase subunit TIM16TIM16_YEAST 16,216.50 11 0 OS = Saccharomyces cerevisiae GN = PAM16 PE =1 SV = 1 Phosphatidate cytidylyltransferase OS = Saccharomycescerevisiae CDS1_YEAST 51,825.70 11 0 GN = CDS1 PE = 1 SV = 1 26Sproteasome regulatory subunit RPN12 OS = Saccharomyces RPN12_YEAST31,922.00 11 0 cerevisiae GN = RPN12 PE = 1 SV = 3 N-terminalacetyltransferase A complex subunit NAT1 NAT1_YEAST 98,912.00 11 0 OS =Saccharomyces cerevisiae GN = NAT1 PE = 1 SV = 2 Nucleolarpre-ribosomal-associated protein 1 OS = Saccharomyces URB1_YEAST203,299.10 11 0 cerevisiae GN = URB1 PE = 1 SV = 2 GU4 nucleic-bindingprotein 1 OS = Saccharomyces cerevisiae G4P1_YEAST 42,084.50 87 4 GN =ARC1 PE = 1 SV = 2 Mitochondrial peculiar membrane protein 1 OS =Saccharomyces cerevisiae MPM1_YEAST 28,471.40 43 2 GN = MPM1 PE = 1 SV =1 6-phosphogluconate dehydrogenase, decarboxylating 1 6PGD1_YEAST53,545.30 494 23 OS = Saccharomyces cerevisiae GN = GND1 PE = 1 SV = 1Transcription-associated protein 1 OS = Saccharomyces cerevisiaeTRA1_YEAST 433,195.70 21 1 GN = TRA1 PE = 1 SV = 1 RNApolymerase-associated protein CTR9 OS = Saccharomyces cerevisiaeCTR9_YEAST 124,663.10 42 2 GN = CTR9 PE = 1 SV = 2 DNA-directed RNApolymerases I, II, and III subunit RPABC3 RPAB3_YEAST 16,512.10 21 1 OS= Saccharomyces cerevisiae GN = RPB8 PE = 1 SV = 1Ribonucleoside-diphosphate reductase large chain 1 RIR1_YEAST 99,564.5021 1 OS = Saccharomyces cerevisiae GN = RNR1 PE = 1 SV = 2 60S ribosomalprotein L10 OS = Saccharomyces cerevisiae GN = RPL10 RL10_YEAST25,362.10 168 8 PE = 1 SV = 1 Sphingolipid long chain base-responsiveprotein PIL1 PIL1_YEAST 38,350.30 166 8 OS = Saccharomyces cerevisiae GN= PIL1 PE = 1 SV = 1 Ribosome-associated complex subunit SSZ1 OS =Saccharomyces SSZ1_YEAST 58,239.50 145 7 cerevisiae GN = SSZ1 PE = 1 SV= 2 Golgin IMH1 OS = Saccharomyces cerevisiae GN = IMH1 PE = 1 SV = 1IMH1_YEAST 105,231.40 10 0 Protein SCO2, mitochondrial OS =Saccharomyces cerevisiae SCO2_YEAST 34,890.60 10 0 GN = SCO2 PE = 1 SV =1 3-ketoacyl-CoA reductase OS = Saccharomyces cerevisiae GN = IFA38MKAR_YEAST 38,709.70 10 0 PE = 1 SV = 1 Iron transport multicopperoxidase FET5 OS = Saccharomyces cerevisiae FET5_YEAST 70,880.90 10 0 GN= FET5 PE = 1 SV = 1 Protein ISD11 OS = Saccharomyces cerevisiae GN =ISD11 PE = 1 SV = 1 ISD11_YEAST 11,266.40 10 0 Mitochondrialdistribution and morphology protein 38 MDM38_YEAST 65,008.10 10 0 OS =Saccharomyces cerevisiae GN = MDM38 PE = 1 SV = 1 Elongation of fattyacids protein 3 OS = Saccharomyces cerevisiae ELO3_YEAST 39,467.00 10 0GN = ELO3 PE = 1 SV = 1 Nucleolar GTP-binding protein 1 OS =Saccharomyces cerevisiae NOG1_YEAST 74,412.80 10 0 GN = NOG1 PE = 1 SV =1 Peptidyl-prolyl cis-trans isomerase ESS1 OS = Saccharomyces cerevisiaeESS1_YEAST 19,404.90 10 0 GN = ESS1 PE = 1 SV = 3 ATPase GET3 OS =Saccharomyces cerevisiae (strain RM11-1a) GET3_YEAS1 39,355.10 10 0 GN =GET3 PE = 3 SV = 1 (+2) Protein APA1 OS = Saccharomyces cerevisiae GN =APA1 PE = 1 SV = 4 APA1_YEAST 36,494.20 10 0 Mitochondrial respiratorychain complexes assembly protein AFG3 AFG3_YEAST 84,547.40 10 0 OS =Saccharomyces cerevisiae GN = AFG3 PE = 1 SV = 1 Calcium-transportingATPase 2 OS = Saccharomyces cerevisiae ATC2_YEAST 130,866.40 10 0 GN =PMC1 PE = 1 SV = 1 Probable intramembrane protease YKL100C OS =Saccharomyces YKK0_YEAST 67,528.20 10 0 cerevisiae GN = YKL100C PE = 1SV = 1 KH domain-containing protein YBL032W OS = Saccharomycescerevisiae YBD2_YEAST 41,684.60 10 0 GN = YBL032W PE = 1 SV = 1Mitochondrial import receptor subunit TOM22 OS = SaccharomycesTOM22_YEAST 16,790.90 10 0 cerevisiae GN = TOM22 PE = 1 SV = 3 ProteinMSP1 OS = Saccharomyces cerevisiae GN = MSP1 PE = 1 SV = 2 MSP1_YEAST40,346.50 10 0 UPF0364 protein YMR027W OS = Saccharomyces cerevisiaeYMR7_YEAST 54,130.90 10 0 GN = YMR027W PE = 1 SV = 1 Uncharacterizedprotein YJL217W OS = Saccharomyces cerevisiae YJV7_YEAST 21,966.80 10 0GN = YJL217W PE = 1 SV = 1 ER membrane protein complex subunit 4 OS =Saccharomyces cerevisiae EMC4_YEAST 21,460.70 10 0 GN = EMC4 PE = 1 SV =1 Sm-like protein LSm1 OS = Saccharomyces cerevisiae GN = LSM1LSM1_YEAST 20,307.60 10 0 PE = 1 SV = 1 Probablealpha-1,6-mannosyltransferase MNN10 OS = Saccharomyces MNN10_YEAST46,750.50 10 0 cerevisiae GN = MNN10 PE = 1 SV = 1 Protein HAM1 OS =Saccharomyces cerevisiae GN = HAM1 PE = 1 SV = 1 HAM1_YEAST 22,093.90 100 NADPH-dependent methylglyoxal reductase GRE2 GRE2_YEAST 38,170.30 10 0OS = Saccharomyces cerevisiae GN = GRE2 PE = 1 SV = 1 Alpha-1,2mannosyltransferase KTR1 OS = Saccharomyces cerevisiae KTR1_YEAST46,023.70 10 0 GN = KTR1 PE = 1 SV = 1 Protein VTH1 OS = Saccharomycescerevisiae GN = VTH1 PE = 1 SV = 1 VTH1_YEAST 174,434.90 10 0 (+1)Trehalose synthase complex regulatory subunit TPS3 TPS3_YEAST 118,837.5010 0 OS = Saccharomyces cerevisiae GN = TPS3 PE = 1 SV = 3 Heat shockprotein 60, mitochondrial OS = Saccharomyces cerevisiae HSP60_YEAST60,753.00 743 38 GN = HSP60 PE = 1 SV = 1 Pyruvate dehydrogenase E1component subunit beta, mitochondrial ODPB_YEAST 40,054.20 77 4 OS =Saccharomyces cerevisiae GN = PDB1 PE = 1 SV = 2 Pyruvate dehydrogenaseE1 component subunit alpha, mitochondrial ODPA_YEAST 46,344.40 96 5 OS =Saccharomyces cerevisiae GN = PDA1 PE = 1 SV = 2 Actin-related protein 3OS = Saccharomyces cerevisiae GN = ARP3 ARP3_YEAST 49,542.70 19 1 PE = 1SV = 1 AMP deaminase OS = Saccharomyces cerevisiae GN = AMD1 PE = 1AMPD_YEAST 93,304.30 19 1 SV = 2 Lon protease homolog, mitochondrial OS= Saccharomyces cerevisiae LONM_YEAST 127,116.80 56 3 GN = PIM1 PE = 1SV = 2 Isocitrate dehydrogenase [NAD] subunit 1, mitochondrialIDH1_YEAST 39,325.30 223 12 OS = Saccharomyces cerevisiae GN = IDH1 PE =1 SV = 2 Serine hydroxymethyltransferase, cytosolic OS = Saccharomycescerevisiae GLYC_YEAST 52,219.70 110 6 GN = SHM2 PE = 1 SV = 2 Rabprotein geranylgeranyltransferase component A RAEP_YEAST 67,374.90 9 0OS = Saccharomyces cerevisiae GN = MRS6 PE = 1 SV = 2 37S ribosomalprotein MRP1, mitochondrial OS = Saccharomyces RT01_YEAST 36,730.90 9 0cerevisiae GN = MRP1 PE = 1 SV = 2 Carboxypeptidase S OS = Saccharomycescerevisiae GN = CPS1 PE = 1 CBPS_YEAST 64,599.30 9 0 SV = 2 Probableglucose transporter HXT5 OS Saccharomyces cerevisiae HXT5_YEAST66,252.90 9 0 GN = HXT5 PE = 1 SV = 1 Glycerol-3-phosphatedehydrogenase, mitochondrial GPDM_YEAST 72,390.60 90 5 OS =Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 Cytochrome b2,mitochondrial OS = Saccharomyces cerevisiae CYB2_YEAST 65,541.20 9 0 GN= CYB2 PE = 1 SV = 1 Translation machinery-associated protein 20 OS =Saccharomyces TMA20_YEAST 20,278.30 9 0 cerevisiae GN = TMA20 PE = 1 SV= 1 D-arabinono-1,4-lactone oxidase OS = Saccharomyces cerevisiaeALO_YEAST 59,494.80 9 0 GN = ALO1 PE = 1 SV = 1 Protein phosphatase 2Chomolog 3 OS = Saccharomyces cerevisiae PP2C3_YEAST 51,391.60 9 0 GN =PTC3 PE = 1 SV = 3 DNA-directed RNA polymerase II subunit RPB9 OS =Saccharomyces RPB9_YEAST 14,288.00 9 0 cerevisiae GN = RPB9 PE = 1 SV =1 Casein kinase II subunit alpha OS = Saccharomyces cerevisiaeCSK21_YEAST 44,669.80 9 0 GN = CKA1 PE = 1 SV = 1 26S proteaseregulatory subunit 6A OS = Saccharomyces cerevisiae PRS6A_YEAST48,257.20 9 0 GN = RPT5 PE = 1 SV = 3 Enoyl reductase TSC13 OS =Saccharomyces cerevisiae GN = TSC13 TSC13_YEAST 36,770.00 9 0 PE = 1 SV= 1 H/ACA ribonucleoprotein complex subunit 2 OS = SaccharomycesNHP2_YEAST 17,122.10 9 0 cerevisiae GN = NHP2 PE = 1 SV = 2 Retrograderegulation protein 2 OS = Saccharomyces cerevisiae RTG2_YEAST 65,573.609 0 GN = RTG2 PE = 1 SV = 2 Uncharacterized protein YDR476 OS =Saccharomyces cerevisiae YD476_YEAST 25,266.70 9 0 GN = YDR476C PE = 1SV = 1 DNA-directed RNA polymerases I and III subunit RPAC2 RPAC2_YEAST16,150.90 9 0 OS = Saccharomyces cerevisiae GN = RPC19 PE = 1 SV = 1 GPItransamidase component GPI16 OS = Saccharomyces cerevisiae GPI16_YEAST68,775.10 9 0 GN = GPI16 PE = 1 SV = 2 V-type proton ATPase subunit e OS= Saccharomyces cerevisiae VA0E_YEAST 8,381.10 9 0 GN = VMA9 PE = 1 SV =1 Cell division control protein 28 OS = Saccharomyces cerevisiaeCDC28_YEAST 34,063.40 18 1 GN = CDC28 PE = 1 SV = 1Serine/threonine-protein phosphatase 2B catalytic subunit A2 PP2B2_YEAST68,529.90 9 0 OS = Saccharomyces cerevisiae GN = CNA2 PE = 1 SV = 2GTP-binding protein YPT31/YPT8 OS = Saccharomyces cerevisiae YPT31_YEAST24,469.90 9 0 GN = YPT31 PE = 1 SV = 3 (+1) FK506-binding nuclearprotein OS = Saccharomyces cerevisiae FKBP3_YEAST 46,554.20 9 0 GN =FPR3 PE = 1 SV = 2 D-3-phosphoglycerate dehydrogenase 2 OS =Saccharomyces cerevisiae SER33_YEAST 51,189.50 9 0 GN = SER33 PE = 1 SV= 1 Coatomer subunit beta OS = Saccharomyces cerevisiae GN = SEC26COPB_YEAST 109,023.60 9 0 PE = 1 SV = 2 Dipeptidyl aminopeptidase B OS =Saccharomyces cerevisiae DAP2_YEAST 93,406.70 9 0 GN = DAP2 PE = 2 SV =2 Protein UTH1 OS = Saccharomyces cerevisiae (strain RM11-1a) UTH1_YEAS136,735.90 9 0 GN = UTH1 PE = 3 SV = 1 (+3) Uncharacterizedoxidoreductase YML125C OS = Saccharomyces cerevisiae YMM5_YEAST35,288.60 9 0 GN = YML125C PE = 1 SV = 1 Long-chain-fatty-acid--CoAligase 3 OS = Saccharomyces cerevisiae LCF3_YEAST 77,948.60 9 0 GN =FAA3 PE = 1 SV = 1 Actin-related protein 2/3 complex subunit 2 OS =Saccharomyces cerevisiae ARPC2_YEAST 39,567.70 18 1 GN = ARC35 PE = 1 SV= 1 Ceramide very long chain fatty acid hydroxylase SCS7 SCS7_YEAST44,882.80 9 0 OS = Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1Protein SDS24 OS = Saccharomyces cerevisiae (strain YJM789) SCS24_YEAS757,188.20 9 0 GN = SDS24 PE = 3 SV = 1 (+1) Cytochrome c oxidaseassembly protein COX14 OS = Saccharomyces COX14_YEAST 7,959.10 9 0cerevisiae GN = COX14 PE = 1 SV = 1 Signal recognition particle subunitSRP14 OS = Saccharomyces cerevisiae SRP14_YEAST 16,430.30 9 0 GN = SRP14PE = 1 SV = 1 Putative guanine nucleotide-exchange factor SED4SED4_YEAST 114,081.60 9 0 OS = Saccharomyces cerevisiae GN = SED4 PE = 1SV = 1 Cytochrome b-c1 complex subunit 1, mitochondrial QCR1_YEAST50,229.00 71 4 OS = Saccharomyces cerevisiae GN = COR1 PE = 1 SV = 1Lysyl-tRNA synthetase, cytoplasmic OS = Saccharomyces cerevisiaeSYKC_YEAST 67,960.50 88 5 GN = KRS1 PE = 1 SV = 2 Glutamyl-tRNAsynthetase, cytoplasmic OS = Saccharomyces cerevisiae SYEC_YEAST80,846.20 246 14 GN = GUS1 PE = 1 SV = 3 Protein transport protein SEC13OS = Saccharomyces cerevisiae SEC13_YEAST 33,042.60 35 2 GN = SEC13 PE =1 SV = 1 Threonyl-tRNA synthetase, cytoplasmic OS = Saccharomycescerevisiae SYTC_YEAST 84,522.60 121 7 GN = THS1 PE = 1 SV = 2Uncharacterized protein YMR178W OS = Saccharomyces cerevisiae YM44_YEAST31,145.60 51 3 GN = YMR178W PE = 1 SV = 1 40S ribosomal protein S25-A OS= Saccharomyces cerevisiae RS25A_YEAST 12,039.90 68 4 GN = RPS25A PE = 1SV = 1 (+1) Transposon Ty2-LR1 Gag-Pol polyprotein OS = Saccharomycescerevisiae YL21B_YEAST 202,130.30 17 1 GN = TY2B-LR1 PE = 3 SV = 1Farnesyl pyrophosphate synthase OS = Saccharomyces cerevisiae FPP2_YEAST40,485.30 135 8 GN = FPP1 PE = 1 SV = 2 Isocitrate dehydrogenase [NAD]subunit 2, mitochondrial IDH2_YEAST 39,740.60 151 9 OS = Saccharomycescerevisiae GN = IDH2 PE = 1 SV = 1 Nascent polypeptide-associatedcomplex subunit beta-1 NACB1_YEAS7 17,020.50 33 2 OS = Saccharomycescerevisiae (strain YJM789) GN = EGD1 PE = 3 (+1) SV = 1 40S ribosomalprotein S3 OS = Saccharomyces cerevisiae GN = RPS3 RS3_YEAST 26,503.00296 18 PE = 1 SV = 5 ATP-dependent RNA helicase SUB2 OS = Saccharomycescerevisiae SUB2_YEAS7 50,280.10 49 3 (strain YJM789) GN = SUB2 PE = 3 SV= 1 (+1) Elongation factor 1-gamma 2 OS = Saccharomyces cerevisiaeEF1G2_YEAST 46,521.90 98 6 GN = TEF4 PE = 1 SV = 1 Fold NSAF NSAFenriched Protein TAL-PrA Wild type TAL-PrA/WT Rank Rank/N Plasmamembrane ATPase 1 OS = Saccharomyces 0.00300044 2.19206E−05 136.87786841 0.001956947 cerevisiae GN = PMA1 PE = 1 SV = 2 Transposon Ty1-HGag-Pol polyprotein OS = 0.000721016 1.07667E−05 66.96712916 20.003913894 Saccharomyces cerevisiae GN = TY1B-H PE = 1 SV = 1ATP-dependent RNA helicase DED1 OS = 0.002132761 3.33122E−05 64.023519083 0.005870841 Saccharomyces cerevisiae (strain YJM789) GN = DED1 PE = 3SV = 1 Protein TIF31 OS = Saccharomyces cerevisiae 0.0008339361.50427E−05 55.43798971 4 0.007827789 GN = TIF31 PE = 1 SV = 1 ProteinURA1 OS = Saccharomyces cerevisiae 0.002963245 5.34515E−05 55.43798971 50.009784736 GN = URA2 PE = 1 SV = 4 Elongation factor 3B OS =Saccharomyces cerevisiae 0.001017068 1.88464E−05 53.96618467 60.011741683 GN = HEF3 PE = 1 SV = 2 Transposon Ty1-OL Gag polyprotein OS= 0.002361064 4.4561E−05 52.98498131 7 0.01369863 Saccharomycescerevisiae GN = TY1A-OL PE = 1 SV = 1 40S ribosomal protein S1-B OS =Saccharomyces 0.003792691 7.57911E−05 50.04137124 8 0.015655577cerevisiae (strain RM11-1a) GN = RPS1B PE = 3 SV = 1 40S ribosomalprotein S1-A OS = Saccharomyces 0.003522263 7.59733E−05 46.36185865 90.017612524 cerevisiae (strain RM11-1a) GN = RPS1A PE = 3 SV = 1Transposon Ty1-DR3 Gag polyprotein OS = 0.002047426 4.43968E−0546.11655781 10 0.019569472 Saccharomyces cerevisiae GN = TY1A-DR3 PE = 1SV = 1 Galactose transporter OS = Saccharomyces cerevisiae 0.0015406853.43213E−05 44.89005361 11 0.021526419 GN = GAL2 PE = 1 SV = 3Argininosuccinate synthase OS = Saccharomyces 0.002019878 4.65214E−0543.41824857 12 0.023483366 cerevisiae GN = ARG1 PE = 1 SV = 2Pleiotropic ABC efflux transporter of multiple drugs 0.0004777121.28122E−05 37.28572759 13 0.025440313 OS = Saccharomyces cerevisiae GN= PDR5 PE = 1 SV = 1 1,3-beta-glucan synthase component FKS1 0.0003764671.01637E−05 37.04042675 14 0.02739726 OS = Saccharomyces cerevisiae GN =FKS1 PE = 1 SV = 2 Heat shock protein SSC3, mitochondrial OS =Saccharomyces cerevisiae GN = ECM10 PE = 1 0.001146459 3.11579E−0536.79512591 15 0.029354207 SV = 1 Pyruvate decarboxylase isozyme 3 OS =Saccharomyces 0.001304785 3.54608E−05 36.79512591 16 0.031311155cerevisiae GN = PDC6 PE = 1 SV = 3 Nuclear segregation protein BFR1 OS =Saccharomyces 0.00134076 3.99651E−05 33.606215 17 0.033268102 cerevisiaeGN = BFR1 PE = 1 SV = 1 60S ribosomal protein L18 OS = Saccharomyces0.003360413 0.000106195 31.64380828 18 0.035225049 cerevisiae GN =RPL18A PE = 1 SV = 1 40S ribosomal protein S2 OS = Saccharomyces0.002458834 7.95536E−05 30.90790577 19 0.037181996 cerevisiae GN = RPS2PE = 1 SV = 3 1,3-beta-glucan synthase component GSC2 0.0003110421.00635E−05 30.90790577 20 0.039138943 OS = Saccharomyces cerevisiae GN= GSC2 PE = 1 SV = 2 6-phosphogluconate dehydrogenase, decarboxylating 20.001172178 4.0496E−05 28.94549905 21 0.04109589 OS = Saccharomycescerevisiae GN = GND2 PE = 1 SV = 1 High-affinity hexose transporter HXT60.00092217 3.48087E−05 26.49249066 22 0.043052838 OS = Saccharomycescerevisiae GN = HXT7 PE = 1 SV = 1 Protein GAL3 OS = Saccharomycescerevisiae GN = GAL3 0.000986018 3.75666E−05 26.24718982 23 0.045009785PE = 1 SV = 2 ATP-dependent RNA helicase MSS116, mitochondrial OS =0.000737438 2.8631E−05 25.75658814 24 0.046966732 Saccharomycescerevisiae GN = MSS116 PE = 1 SV = 1 Probable cation-transporting ATPase1 0.000388073 1.61431E−05 24.03948226 25 0.048923679 OS = Saccharomycescerevisiae GN = SPF1 PE = 1 SV = 1 High-affinity hexose transporter HXT60.000837185 3.48254E−05 24.03948226 26 0.050880626 OS = Saccharomycescerevisiae GN = HXT6 PE = 1 SV = 2 Eukaryotic translation initiationfactor 5B OS = 0.000467585 1.94507E−05 24.03948226 26 0.050880626Saccharomyces cerevisiae GN = FUN12 PE = 1 SV = 2 DNA-directed RNApolymerase II subunit RPB1 0.000268377 1.13966E−05 23.54888058 280.054794521 OS = Saccharomyces cerevisiae GN = RPB1 PE = 1 SV = 21,3-beta-glucanosyltransferase GAS1 OS = 0.0008451 3.66506E−0523.0582789 29 0.056751468 Saccharomyces cerevisiae GN = GAS1 PE = 1 SV =2 Eukaryotic translation initiation factor 3 subunit B 0.000565272.47784E−05 22.81297806 30 0.058708415 OS = Saccharomyces cerevisiae(strain YJM789) Phosphoglucomutase-1 OS = Saccharomyces cerevisiae0.000772352 3.45999E−05 22.32237639 31 0.060665362 GN = PGM1 PE = 1 SV =1 T-complex protein 1 subunit gamma 0.000819711 3.71295E−05 22.0770755532 0.062622309 OS = Saccharomyces cerevisiae GN = CCT3 PE = 1 SV = 2FACT complex subunit SPT16 OS = Saccharomyces 0.000397347 1.84072E−0521.58647387 33 0.064579256 cerevisiae GN = SPT16 PE = 1 SV = 1ATP-dependent RNA helicase DBP1 0.000685433 3.21179E−05 21.34117303 340.066536204 OS = Saccharomyces cerevisiae (strain YJM789) GN = DBP1 PE =3 SV = 1 Dihydrolipoyllysine-residue acetyltransferase component0.00089935 4.21415E−05 21.34117303 34 0.066536204 of pyruvatedehydrogenase complex, mitochondrial OS = Saccharomyces cerevisiae GN =PDA2 PE = 1 SV = 1 Clathrin heavy chain OS = Saccharomyces cerevisiae0.000494931 2.33254E−05 21.21852261 36 0.070450098 GN = CHC1 PE = 1 SV =1 40S ribosomal protein S8 OS = Saccharomyces 0.002048356 9.70975E−0521.09587219 37 0.072407045 cerevisiae GN = RPS8A PE = 1 SV = 3DNA-directed RNA polymerase II subunit RPB2 0.000328146 1.5738E−0520.85057135 38 0.074363992 OS = Saccharomyces cerevisiae GN = RPB2 PE =1 SV = 2 Glutamine synthetase OS = Saccharomyces cerevisiae 0.001026035.22842E−05 19.62406715 39 0.076320939 GN = GLN1 PE = 1 SV = 2Mitochondrial import receptor subunit TOM40 OS = 0.001006641 5.19456E−0519.37876631 40 0.078277886 Saccharomyces cerevisiae GN = TOM40 PE = 1 SV= 1 C-1-tetrahydrofolate synthase, cytoplasmic 0.000398323 2.1366E−0518.64286379 41 0.080234834 OS = Saccharomyces cerevisiae GN = ADE3 PE =1 SV = 1 rRNA 2′-O-methyltransferase fibrillarin 0.001165684 6.33608E−0518.39756296 42 0.082191781 OS = Saccharomyces cerevisiae GN = NOP1 PE =1 SV = 1 Protein SCP160 OS = Saccharomyces cerevisiae 0.0011920426.47935E−05 18.39756296 42 0.082191781 GN = SCP160 PE = 1 SV = 3 Proteintransport protein SEC23 OS = Saccharomyces 0.000457965 2.55747E−0517.90696128 44 0.086105675 cerevisiae GN = SEC23 PE = 1 SV = 1 Nucleolarprotein 56 OS = Saccharomyces cerevisiae 0.000687645 3.8401E−0517.90696128 45 0.088062622 GN = NOP56 PE = 1 SV = 1 Orotidine5′-phosphate decarboxylase 0.001300706 7.4683E−05 17.4163596 460.090019569 OS = Saccharomyces cerevisiae GN = URA3 PE = 1 SV = 2Homocitrate synthase, cytosolic isozyme OS = 0.000773374 4.63641E−0516.68045708 47 0.091976517 Saccharomyces cerevisiae GN = LYS20 PE = 1 SV= 2 External NADH-ubiquinone oxidoreductase 1, 0.000571718 3.47863E−0516.43515624 48 0.093933464 mitochondrial OS = Saccharomyces cerevisiaeGN = NDE1 PE = 1 SV = 1 Eukaryotic translation initiation factor 3subunit C 0.000384987 2.34246E−05 16.43515624 49 0.095890411 OS =Saccharomyces cerevisiae (strain YJM789) GN = NIP1 PE = 3 SV = 1 ZuotinOS = Saccharomyces cerevisiae GN = ZUO1 PE = 1 0.00072121 4.4547E−0516.1898554 50 0.097847358 SV = 1 Trehalose-phosphatase OS =Saccharomyces cerevisiae 0.000327715 2.12059E−05 15.45395288 510.099804305 GN = TPS2 PE = 1 SV = 3 Saccharopepsin OS = Saccharomycescerevisiae 0.000758359 4.90722E−05 15.45395288 51 0.099804305 GN = PEP4PE = 1 SV = 1 rRNA biogenesis protein RRP5 OS = Saccharomyces0.000174731 1.13065E−05 15.45395288 53 0.1037182 cerevisiae GN = RRP5 PE= 1 SV = 1 cAMP-dependent protein kinase regulatory subunit 0.0007033434.62462E−05 15.20865204 54 0.105675147 OS = Saccharomyces cerevisiae GN= BCY1 PE = 1 SV = 4 Galactokinase OS = Saccharomyces cerevisiae0.012480213 0.000829109 15.05255151 55 0.107632094 GN = GAL1 PE = 1 SV =4 Probable 2-methylcitrate dehydratase 0.000566456 3.78562E−0514.9633512 56 0.109589041 OS = Saccharomyces cerevisiae GN = PDH1 PE = 1SV = 1 2-isopropylmalate synthase 2, mitochondrial 0.0004862493.2496E−05 14.9633512 57 0.111545988 OS = Saccharomyces cerevisiae GN =LEU9 PE = 1 SV = 1 NADH-cytochrome b5 reductase 2 OS = Saccharomyces0.000957996 6.40228E−05 14.9633512 58 0.113502935 cerevisiae (strainYJM789) GN = MCR1 PE = 2 SV = 1 6,7-dimethyl-8-ribityllumazine synthase0.001732121 0.000117687 14.71805036 59 0.115459883 OS = Saccharomycescerevisiae GN = RIB4 PE = 1 SV = 2 N-(5′-phosphoribosyl)anthranilateisomerase 0.001331159 9.0444E−05 14.71805036 59 0.115459883 OS =Saccharomyces cerevisiae GN = TRP1 PE = 1 SV = 2 Glutamate synthase[NADH] OS = Saccharomyces 0.000130484 9.17129E−06 14.22744869 610.119373777 cerevisiae GN = GLT1 PE = 1 SV = 2 Nuclear localizationsequence-binding protein 0.000661538 4.90335E−05 13.49154617 620.121330724 OS = Saccharomyces cerevisiae GN = NSR1 PE = 1 SV = 1 V-typeproton ATPase subunit a, vacuolar isoform 0.000308399 2.28587E−0513.49154617 62 0.121330724 OS = Saccharomyces cerevisiae GN = VPH1 PE =1 SV = 3 4-aminobutyrate aminotransferase OS = Saccharomyces 0.0005564324.1243E−05 13.49154617 64 0.125244618 cerevisiae GN = UGA1 PE = 1 SV = 2Dihydroorotate dehydrogenase OS = Saccharomyces 0.000831161 6.27469E−0513.24624533 65 0.127201566 cerevisiae GN = URA1 PE = 1 SV = 1 Eukaryotictranslation initiation factor 2A OS = 0.000405663 3.06247E−0513.24624533 66 0.129158513 Saccharomyces cerevisiae GN = YGR054W PE = 1SV = 1 60S ribosomal protein L32 OS = Saccharomyces 0.001921970.000147833 13.00094449 67 0.13111546 cerevisiae GN = RPL32 PE = 1 SV =1 60S ribosomal protein L15-A OS = Saccharomyces 0.002303041 0.00017883112.87829407 68 0.133072407 cerevisiae GN = RPL15A PE = 1 SV = 3Mitochondrial import receptor subunit TOM70 0.000389569 3.11398E−0512.51034281 69 0.135029354 OS = Saccharomyces cerevisiae (strain YJM789)GN = TOM70 PE = 3 SV = 1 Mitochondrial acidic protein MAM33 OS =0.000906643 7.24715E−05 12.51034281 70 0.136986301 Saccharomycescerevisiae GN = MAM33 PE = 1 SV = 1 H/ACA ribonucleoprotein complexsubunit 4 0.000499387 3.99179E−05 12.51034281 70 0.136986301 OS =Saccharomyces cerevisiae GN = CBF5 PE = 1 SV = 1 60S ribosomal proteinL8-A OS = Saccharomyces 0.003828248 0.000310574 12.32636718 720.140900196 cerevisiae GN = RPL8A PE = 1 SV = 4 Eukaryotic translationinitiation factor 2 subunit alpha 0.000771455 6.28987E−05 12.26504197 730.142857143 OS = Saccharomyces cerevisiae GN = SUI2 PE = 1 SV = 1NADPH--cytochrome P450 reductase 0.000348866 2.84439E−05 12.26504197 740.14481409 OS = Saccharomyces cerevisiae GN = NCP1 PE = 1 SV = 3Nucleolar protein 58 OS = Saccharomyces cerevisiae 0.0009216417.66773E−05 12.01974113 75 0.146771037 (strain YJM789) GN = NOP58 PE = 3SV = 1 60S ribosomal protein L14-B OS = Saccharomyces 0.0034290320.000288224 11.89709071 76 0.148727984 cerevisiae GN = RPL14B PE = 1 SV= 1 Pentafunctional AROM polypeptide OS = Saccharomyces 0.000297332.49918E−05 11.89709071 76 0.148727984 cerevisiae GN = ARO1 PE = 1 SV =1 60S ribosomal protein L8-B OS = Saccharomyces 0.00367754 0.00031071411.8357655 78 0.152641879 cerevisiae GN = RPL8B PE = 1 SV = 3GTP-binding protein RHO1 OS = Saccharomyces 0.001110598 9.43228E−0511.77444029 79 0.154598826 cerevisiae GN = RHO1 PE = 1 SV = 3 Invertase2 OS = Saccharomyces cerevisiae GN = SUC2 0.000424013 3.60113E−0511.77444029 80 0.156555773 PE = 1 SV = 1 Squalene synthase OS =Saccharomyces cerevisiae 0.000497125 4.22207E−05 11.77444029 800.156555773 GN = ERG9 PE = 1 SV = 2 Eukaryotic translation initiationfactor 3 subunit B 0.000577426 4.95569E−05 11.65178987 82 0.160469667 OS= Saccharomyces cerevisiae GN = PRT1 PE = 1 SV = 1 Cytochrome c iso-2 OS= Saccharomyces cerevisiae 0.00200888 0.000174244 11.52913945 830.162426614 GN = CYC7 PE = 1 SV = 1 ATP-dependent permease PDR15 OS =Saccharomyces 0.000146155 1.2677E−05 11.52913945 84 0.164383562cerevisiae GN = PDR15 PE = 1 SV = 1 60S ribosomal protein L28 OS =Saccharomyces 0.001473501 0.000130585 11.28383861 85 0.166340509cerevisiae GN = RPL28 PE = 1 SV = 2 Methionyl-tRNA synthetase,cytoplasmic 0.000287593 2.54871E−05 11.28383861 86 0.168297456 OS =Saccharomyces cerevisiae GN = MES1 PE = 1 SV = 4 Eukaryotic translationinitiation factor 3 subunit G 0.000790304 7.1595E−05 11.03853777 870.170254403 OS = Saccharomyces cerevisiae GN = TIF35 PE = 1 SV = 1General transcriptional corepressor TUP1 0.000307833 2.78871E−0511.03853777 88 0.17221135 OS = Saccharomyces cerevisiae GN = TUP1 PE = 1SV = 2 Heat shock protein 42 OS = Saccharomyces cerevisiae 0.0005504725.10016E−05 10.79323693 89 0.174168297 GN = HSP42 PE = 1 SV = 1 60Sribosomal protein L15-B OS = Saccharomyces 0.001842433 0.00017883110.30263526 90 0.176125245 cerevisiae GN = RPL15B PE = 1 SV = 2 40Sribosomal protein S23 OS = Saccharomyces 0.001402798 0.00013615910.30263526 90 0.176125245 cerevisiae GN = RPS23A PE = 1 SV = 1T-complex protein 1 subunit theta OS = Saccharomyces 0.0003648593.54141E−05 10.30263526 92 0.180039139 cerevisiae GN = CCT8 PE = 1 SV =1 26S protease regulatory subunit 8 homolog 0.000485124 4.82358E−0510.05733442 93 0.181996086 OS = Saccharomyces cerevisiae GN = RPT6 PE =1 SV = 4 SDO1-like protein YHR087W OS = Saccharomyces 0.0018287410.000181832 10.05733442 94 0.183953033 cerevisiae GN = YHR087W PE = 1 SV= 1 Mitochondrial escape protein 2 OS = Saccharomyces 0.0002216022.25847E−05 9.812033576 95 0.18590998 cerevisiae GN = YME2 PE = 1 SV = 1Alpha-soluble NSF attachment protein OS = 0.000653179 6.65692E−059.812033576 95 0.18590998 Saccharomyces cerevisiae GN = SEC17 PE = 1 SV= 4 Protein translocation protein SEC63 OS = 0.000284375 2.89823E−059.812033576 95 0.18590998 Saccharomyces cerevisiae GN = SEC63 PE = 1 SV= 2 Delta-1-pyrroline-5-carboxylate dehydrogenase, 0.0003325263.38896E−05 9.812033576 98 0.191780822 mitochondrial OS = Saccharomycescerevisiae GN = PUT2 PE = 1 SV = 2 Polyamine N-acetyltransferase 1 OS =Saccharomyces 0.001928069 0.000198988 9.689383157 99 0.193737769cerevisiae GN = PAA1 PE = 1 SV = 1 40S ribosomal protein S22-B OS =Saccharomyces 0.002893283 0.000298603 9.689383157 99 0.193737769cerevisiae GN = RPS22B PE = 1 SV = 3 Phosphoinositide phosphatase SAC10.000286194 3.07028E−05 9.321431897 101 0.197651663 OS = Saccharomycescerevisiae GN = SAC1 PE = 1 SV = 1 40S ribosomal protein S26-A OS =Saccharomyces 0.001507278 0.0001617 9.321431897 101 0.197651663cerevisiae GN = RPS26A PE = 1 SV = 1 26S proteasome regulatory subunitRPN2 0.000390567 4.18999E−05 9.321431897 101 0.197651663 OS =Saccharomyces cerevisiae GN = RPN2 PE = 1 SV = 4 Translational activatorGCN1 OS = Saccharomyces 6.86049E−05 7.35991E−06 9.321431897 1010.197651663 cerevisiae GN = GCN1 PE = 1 SV = 1Dolichyl-diphosphooligosaccharide--protein 0.000249663 2.67838E−059.321431897 105 0.205479452 glycosyltransferase subunit STT3 OS =Saccharomyces cerevisiae GN = STT3 PE = 1 SV = 21,3-beta-glucanosyltransferase GAS5 0.000392433 4.21001E−05 9.321431897105 0.205479452 OS = Saccharomyces cerevisiae GN = GAS5 PE = 1 SV = 1Acyl-CoA-binding protein OS = Saccharomyces 0.002023076 0.0002170359.321431897 107 0.209393346 cerevisiae GN = ACB1 PE = 1 SV = 3Tricalbin-1 OS = Saccharomyces cerevisiae GN = TCB1 0.0001483751.63478E−05 9.076131058 108 0.211350294 PE = 1 SV = 1 NADP-specificglutamate dehydrogenase 2 0.000399377 4.4003E−05 9.076131058 1080.211350294 OS = Saccharomyces cerevisiae GN = GDH3 PE = 1 SV = 1Dolichyl-phosphate-mannose--protein 0.00021386 2.35629E−05 9.076131058110 0.215264188 mannosyltransferase 1 OS = Saccharomyces cerevisiae GN =PMT1 PE = 1 SV = 1 Mitochondrial import inner membrane translocase0.001923423 0.000211921 9.076131058 110 0.215264188 subunit TIM10 OS =Saccharomyces cerevisiae GN = MRS11 PE = 1 SV = 1 Ornithinecarbamoyltransferase OS = Saccharomyces 0.000523699 5.77006E−059.076131058 110 0.215264188 cerevisiae GN = ARG3 PE = 1 SV = 1 Putativemagnesium-dependent phosphatase YER134C 0.000943354 0.0001068258.830830219 113 0.221135029 OS = Saccharomyces cerevisiae GN = YER134CPE = 1 SV = 1 Eukaryotic translation initiation factor 4B 0.0003974334.50051E−05 8.830830219 113 0.221135029 OS = Saccharomyces cerevisiae GN= TIF3 PE = 1 SV = 1 Mitochondrial escape protein 2 OS = Saccharomyces0.000199503 2.25917E−05 8.830830219 115 0.225048924 cerevisiae (strainYJM789) GN = YME2 PE = 3 SV = 1 Vesicle-associated membraneprotein-associated protein 0.000716233 8.11059E−05 8.830830219 1150.225048924 SCS2 OS = Saccharomyces cerevisiae GN = SCS2 PE = 1 SV = 3Importin beta SMX1 OS = Saccharomyces cerevisiae 0.000177883 2.01434E−058.830830219 115 0.225048924 GN = SXM1 PE = 1 SV = 1 Inorganic phosphatetransport protein PHO88 OS = 0.000912311 0.00010331 8.830830219 1150.225048924 Saccharomyces cerevisiae GN = PHO88 PE = 1 SV = 1Transcription elongation factor SPT6 0.000225986 2.5951E−05 8.708179799119 0.232876712 OS = Saccharomyces cerevisiae GN = SPT6 PE = 1 SV = 1T-complex protein 1 subunit delta OS = Saccharomyces 0.0003254673.79088E−05 8.585529379 120 0.234833659 cerevisiae GN = CCT4 PE = 1 SV =2 5′-3′ exoribonuclease 1 OS = Saccharomyces cerevisiae 0.00021372.48907E−05 8.585529379 120 0.234833659 GN = KEM1 PE = 1 SV = 1 Fumaratereductase OS = Saccharomyces cerevisiae 0.000368743 4.29494E−058.585529379 122 0.238747554 GN = YEL047C PE = 1 SV = 13-hydroxy-3-methylglutaryl-coenzyme A reductase 1 OS = 0.0001575131.88859E−05 8.34022854 123 0.240704501 Saccharomyces cerevisiae GN =HMG1 PE = 1SV = 1 26S proteasome regulatory subunit RPN9 OS =0.000397789 4.76952E−05 8.34022854 123 0.240704501 Saccharomycescerevisiae GN = RPN9 PE = 1 SV = 1 Dolichyl-phosphate-mannose--protein0.000209652 2.51375E−05 8.34022854 123 0.240704501 mannosyltransferase 2OS = Saccharomyces cerevisiae GN = PMT2 PE = 1 SV = 2 Bifunctionalprotein GAL10 OS = Saccharomyces 0.006432474 0.000781936 8.226338864 1260.246575342 cerevisiae GN = GAL10 PE = 1 SV = 2 ATP-dependent bile acidpermease OS = Saccharomyces 9.3446E−05 1.15438E−05 8.0949277 1270.24853229 cerevisiae GN = YBT1 PE = 1 SV = 2 Saccharopine dehydrogenase[NAD+, L-lysine-forming] 0.000426308 5.26636E−05 8.0949277 1270.24853229 OS = Saccharomyces cerevisiae GN = LYS1 PE = 1 SV = 3Coatomer subunit gamma OS = Saccharomyces 0.000163509 2.08302E−057.849626861 129 0.252446184 cerevisiae GN = SEC21 PE = 1 SV = 2 Celldivision control protein 53 OS = Saccharomyces 0.000182456 2.3244E−057.849626861 129 0.252446184 cerevisiae GN = CDC53 PE = 1 SV = 1Rotenone-insensitive NADH-ubiquinone oxidoreductase, 0.0002994043.81424E−05 7.849626861 131 0.256360078 mitochondrial OS = Saccharomycescerevisiae GN = NDI1 PE = 1 SV = 1 Argininosuccinate lyase OS =Saccharomyces cerevisiae 0.000329703 4.20024E−05 7.84962681 1310.256360078 GN = ARG4 PE = 1 SV = 2 Zinc finger protein GIS2 OS =Saccharomyces cerevisiae 0.000970965 0.000127686 7.604326022 1330.260273973 GN = GIS2 PE = 1 SV = 1 Protein kinase MCK1 OS =Saccharomyces cerevisiae 0.000384952 5.06228E−05 7.604326022 1330.260273973 GN = MCK1 PE = 1 SV = 1 Malate dehydrogenase, peroxisomal OS= 0.000446552 5.87235E−05 7.604326022 135 0.264187867 Saccharomycescerevisiae GN = MDH3 PE = 1 SV = 3 T-complex protein 1 subunit zeta OS =Saccharomyces 0.000277109 3.6441E−05 7.604326022 136 0.266144814cerevisiae GN = CCT6 PE = 1 SV = 1 ATP-dependent RNA helicase DBP2 OS =0.000263443 3.57987E−05 7.359025182 137 0.268101761 Saccharomycescerevisiae GN = DBP2 PE = 1 SV = 1 Cytochrome B pre-mRNA-processingprotein 6 OS = 0.000860311 0.000116906 7.359025182 138 0.270058708Saccharomyces cerevisiae GN = CBP6 PE = 1 SV = 1 Protein DCS2 OS =Saccharomyces cerevisiae 0.000392517 5.33382E−05 7.359025182 1380.270058708 GN = DCS2 PE = 1 SV = 3 Eukaryotic translation initiationfactor 3 subunit A OS = 0.000854379 0.000118738 7.195491289 1400.273972603 Saccharomyces cerevisiae GN = TIF32 PE = 1 SV = 1Glucose-signaling factor 2 OS = Saccharomyces 0.000677298 9.521E−057.113724343 141 0.27592955 cerevisiae GN = GSF2 PE = 1 SV = 1Glycerol-3-phoshate dehydrogenase [NAD+] 2, 0.000314327 4.41859E−057.113724343 142 0.277886497 mitochondrial OS = Saccharomyces cerevisiaeGN = GPD2 PE = 1 SV = 2 Prohibitin-2 OS = Saccharomyces cerevisiae GN =PHB2 0.000451495 6.34682E−05 7.113724343 142 0.277886497 PE = 1 SV = 240S ribosomal protein S29-A OS = Saccharomyces 0.002332289 0.0003278587.113724343 142 0.277886497 cerevisiae GN = RPS29A PE = 1 SV = 3DNA-directed RNA polymerase I subunit RPA1 OS = 8.33248E−05 1.17132E−057.113724343 145 0.283757339 Saccharomyces cerevisiae GN = RPA1 PE = 1 SV= 2 Protein transport protein SEC24 OS = Saccharomyces 0.0001498932.10709E−05 7.113724343 145 0.283757339 cerevisiae GN = SEC24 PE = 1 SV= 1 Carboxypeptidase Y OS = Saccharomyces cerevisiae 0.0002508043.65156E−05 6.868423503 147 0.287671233 GN = PRC1 PE = 1 SV = 1 V-typeproton ATPase subunit d OS = Saccharomyces 0.000376931 5.48789E−056.868423503 148 0.28962818 cerevisiae GN = VMA6 PE = 1 SV = 2Uncharacterized protein YJL171C OS = Saccharomyces 0.0003486965.0768E−05 6.868423503 148 0.28962818 cerevisiae GN = YJL171C PE = 1 SV= 1 Vacuolar protein sorting/targeting protein PEP1 8.43666E−051.22833−E05 6.868423503 148 0.28962818 OS = Saccharomyces cerevisiae GN= PEP1 PE = 1 SV = 1 FACT complex subunit POB3 OS = Saccharomyces0.000238097 3.46655E−05 6.868423503 151 0.295499022 cerevisiae GN = POB3PE = 1 SV = 1 Uncharacterized mitochondrial membrane protein 0.0005415027.88393E−05 6.868423503 151 0.295499022 FMP10 OS = Saccharomycescerevisiae GN = FMP10 PE = 1 SV = 1 RNA annealing protein YRA1 OS =Saccharomyces 0.000579546 8.75034E−05 6.623122664 153 0.299412916cerevisiae GN = YRA1 PE = 1 SV = 2 Mitochondrial outer membrane proteinOM45 OS = 0.000324421 4.8983E−05 6.623122664 154 0.301369863Saccharomyces cerevisiae GN = OM45 PE = 1 SV = 2 Mitochondrial importreceptor subunit TOM5 0.002416716 0.000364891 6.623122664 1540.301369863 OS = Saccharomyces cerevisiae GN = TOM5 PE = 1 SV = 1T-complex protein 1 subunit alpha OS = Saccharomyces 0.0002391333.61058E−05 6.623122664 156 0.305283757 cerevisiae GN = TCP1 PE = 1 SV =2 Eukaryotic translation initiation factor 1A 0.0007988 0.0001252476.377821825 157 0.307240705 OS = Saccharomyces cerevisiae GN = TIF11 PE= 1 SV = 1 Protein MSN5 OS = Saccharomyces cerevisiae 9.79948E−051.53649E−05 6.377821825 158 0.309197652 GN = MSN5 PE = 1 SV = 1 Putativefatty aldehyde dehydrogenase HFD1 0.000232197 3.6407E−05 6.377821825 1580.309197652 OS = Saccharomyces cerevisiae GN = HFD1 PE = 1 SV = 1Ergosterol biosynthetic protein 28 OS = Saccharomyces 0.000812780.000127439 6.377821825 158 0.309197652 cerevisiae GN = ERG28 PE = 1 SV= 1 Protein YRO2 OS = Saccharomyces cerevisiae 0.000359689 5.63969E−056.377821825 158 0.309197652 GN = YRO2 PE = 1 SV = 1Methylene-fatty-acyl-phospholid synthase 0.000601597 9.43265E−056.377821825 162 0.310702544 OS = Saccharomyces cerevisiae GN = PEM2 PE =1 SV = 1 Protein MKT1 OS = Saccharomyces cerevisiae 0.0001417152.31087E−05 6.132520985 163 0.318982387 GN = MKT1 PE = 1 SV = 2 ProteinMRH1 OS = Saccharomyces cerevisiae 0.000370021 6.03376E−05 6.132520985163 0.318982387 GN = MRH1 PE = 1 SV = 1 Eukaryotic translationinitiation factor 2 subunit beta 0.000424122 6.91596E−05 6.132520985 1650.322896282 OS = Saccharomyces cerevisiae GN = SUI3 PE = 1 SV = 2Peroxiredoxin TSA2 OS = Saccharomyces cerevisiae 0.000594774 0.0001010285.887220146 166 0.324853229 GN = TSA2 PE = 1 SV = 3 Endoplasmicreticulum vesicle protein 25 OS = 0.000533314 9.05884E−05 5.887220146166 0.324853229 Saccharomyces cerevisiae GN = ERV25 PE = 1 SV = 1PKHD-type hydroxylase TPA1 OS = Saccharomyces 0.000173629 2.94925E−055.887220146 166 0.324853229 cerevisiae GN = TPA1 PE = 1 SV = 1SED5-binding protein 3 OS = Saccharomyces cerevisiae 0.0001236742.10071E−05 5.887220146 169 0.33072407 GN = SFB3 PE = 1 SV = 1 D-lactatedehydrogenase [cytochrome] 3 0.000232791 3.95417E−05 5.887220146 1690.33072407 OS = Saccharomyces cerevisiae GN = DLD3 PE = 1 SV = 1Single-stranded nucleic acid-binding protein 0.00076317 0.000132395.764569726 171 0.334637965 OS = Saccharomyces cerevisiae GN = SBP1 PE =1 SV = 2 Protein CWH43 OS = Saccharomyces cerevisiae 0.0001141982.02411E−05 5.641919306 172 0.336594912 GN = CWH43 PE = 1 SV = 2T-complex protein 1 subunit eta OS = Saccharomyces 0.0002062473.65562E−05 5.641919306 172 0.336594912 cerevisiae GN = CCT7 PE = 1 SV =1 26S protease regulatory subunit 6B homolog 0.000256832 4.55221E−055.641919306 172 0.336594912 OS = Saccharomyces cerevisiae GN = RPT3 PE =1 SV = 1 NADH-cytochrome b5 reductase 1 OS = Saccharomyces 0.0003911956.93372E−05 5.641919306 172 0.336594912 cerevisiae GN = CBR1 PE = 1 SV =2 Glycogen debranching enzyme OS = Saccharomyces 0.000140824 2.49603E−055.641919306 176 0.344422701 cerevisiae GN = GDB1 PE = 1 SV = 1 C-5sterol desaturase OS = Saccharomyces cerevisiae 0.000288325 5.1104E−055.641919306 176 0.344422701 GN = ERG3 PE = 1 SV = 1 13 kDaribonucleoprotein-associated protein OS = 0.00090797 0.0001609335.641919306 176 0.344422701 Saccharomyces cerevisiae GN = SNU13 PE = 1SV = 1 UPF0202 protein KRE33 OS = Saccharomyces 0.000103228 1.82965E−055.641919306 176 0.344422701 cerevisiae GN = KRE33 PE = 1 SV = 1 Proteinphosphatase PP2A regulatory subunit A 0.00017364 3.07768E−05 5.641919306176 0.344422701 OS = Saccharomyces cerevisiae GN = TPD3 PE = 1 SV = 2Eukaryotic translation initiation factor 2 subunit gamma 0.0002129123.77375E−05 5.641919306 176 0.344422701 OS = Saccharomyces cerevisiae GN= GCD11 PE = 1 SV = 1 Midasin OS = Saccharomyces cerevisiae GN = MDN12.20277E−05 3.90429E−06 5.641919306 182 0.356164384 PE = 1 SV = 1Galactose-1-phosphate uridylyltransferase OS = 0.005800888 0.0010304165.629654264 183 0.358121331 Saccharomyces cerevisiae GN = GAL7 PE = 1 SV= 4 UPF0121 membrane protein YLL023C OS = 0.000366131 6.78446E−055.396618467 184 0.360078278 Saccharomyces cerevisiae GN = YLL023C PE = 1SV = 1 Phosphatidylinositol transfer protein PDR16 OS = 0.0002894445.36342E−05 5.396618467 184 0.360078278 Saccharomyces cerevisiae GN =PDR16 PE = 1 SV = 1 60S ribosomal protein L43 OS = Saccharomyces0.001167888 0.000216411 5.396618467 186 0.363992172 cerevisiae GN =RPL43A PE = 1 SV = 2 Arginine biosynthesis bifunctional protein ARG7,0.000246288 4.56375E−05 5.396618467 186 0.363992172 mitochondrial OS =Saccharomyces cerevisiae GN = ARG7 PE = 1 SV = 1 Probable family 17glucosidase SCW4 OS = 0.00029336 5.436E−05 5.396618467 186 0.363992172Saccharomyces cerevisiae GN = SCW4 PE = 1 SV = 1 26S protease subunitRPT4 OS = Saccharomyces 0.000238513 4.41967E−05 5.396618467 1890.369863014 cerevisiae GN = RPT4 PE = 1 SV = 4 60S ribosomal protein L3OS = Saccharomyces 0.002680969 0.000499055 5.372088383 190 0.371819961cerevisiae GN = RPL3 PE = 1 SV = 4 Phosphoglucamutase-2 OS =Saccharomyces cerevisiae 0.002929237 0.000553804 5.28929935 1910.373776908 GN = PGM2 PE = 1 SV = 1 Uncharacterized phosphatase YNL010WOS = 0.000838173 0.000158927 5.273968047 192 0.375733855 Saccharomycescerevisiae GN = YNL010W PE = 1 SV = 1 Elongation factor 3A OS =Saccharomyces cerevisiae 0.004119318 0.000790698 5.209722589 1930.377690802 GN = YEF3 PE = 1 SV = 3 Casein kinase II subunit alpha’ OS =Saccharomyces 0.000285478 5.54184E−05 5.151317628 194 0.37964775cerevisiae GN = CKA2 PE = 1 SV = 2 54S ribosomal protein L12,mitochondrial OS = 0.000544737 0.000105747 5.151317628 194 0.37964775Saccharomyces cerevisiae GN = MNP1 PE = 1 SV = 1 Nuclear protein SNF4 OS= Saccharomyces cerevisiae 0.000309024 5.99893E−05 5.151317628 1940.37964775 GN = SNF4 PE = 1 SV = 1 Eukaryotic initiation factor 4Fsubunit p150 OS = 0.000105031 2.03892E−05 5.151317628 194 0.37964775Saccharomyces cerevisiae GN = TIF4631 PE = 1 SV = 2 Medium-chain fattyacid ethyl ester synethase/esterase 2 0.000219468 4.26042E−055.151317628 194 0.37964775 OS = Saccharomyces cerevisiae GN = EHT1 PE =1 SV = 1 ABC transporter ATP-binding protein ARB1 OS = 0.0001645123.19359E−05 5.151317628 194 0.37964775 Saccharomyces cerevisiae GN =ARB1 PE = 1 SV = 1 Cysteinyl-tRNA synthetase OS = Saccharomyces0.000128513 2.49476E−05 5.151317628 194 0.37964775 cerevisiae GN =YNL247W PE = 1 SV = 1 Protein TTP1 OS = Saccharomyces cerevisiae GN =TTP1 0.000165973 3.22195E−05 5.151317628 194 0.37964775 PE = 1 SV = 126S proteasome regulatory subunit RPN8 OS = 0.000293607 5.69966E−055.151317628 194 0.37964775 Saccharomyces cerevisiae GN = RPN8 PE = 1 SV= 3 NADH-cytochrome b5 reductase 1 OS = Saccharomyces 0.0003579996.94965E−05 5.151317628 194 0.37964775 cerevisiae (strain YJM789) GN =CBR1 PE = 2 SV = 2 ER membrane protein complex subunit 1 OS =0.000129027 2.50474E−05 5.151317628 204 0.399217221 Saccharomycescerevisiae GN = EMC1 PE = 1 SV = 1 Heat shock protein 78, mitochondrialOS = 0.001712467 0.00033471 5.11627465 205 0.401174168 Saccharomycescerevisiae GN = HSP78 PE = 1 SV = 2 Nuclear protein STH1/NPS1 OS =Saccharomyces 6.83479E−05 1.39314E−05 4.906016788 206 0.403131115cerevisiae GN = STH1 PE = 1 SV = 1 mRNA-binding protein PUF3 OS =Saccharomyces 0.000109244 2.22674E−05 4.906016788 206 0.403131115cerevisiae GN = PUF3 PE = 1 SV = 1 Actin-interacting protein 1 OS =Saccharomyces 0.00015913 3.24356E−05 4.906016788 206 0.403131115cerevisiae GN = AIP1 PE = 1 SV = 1 Cytochrome c iso-1 OS = Saccharomycescerevisiae 0.003517692 0.000717016 4.906016788 206 0.403131115 GN = CYC1PE = 1 SV = 2 CTP synthase 1 OS = Saccharomyces cerevisiae 0.0001655593.37461E−05 4.906016788 206 0.403131115 GN = URA7 PE = 1 SV = 2 Squalenemonooxygenase OS = Saccharomyces 0.000194343 3.96131E−05 4.906016788 2060.403131115 cerevisiae GN = ERG1 PE = 1 SV = 2 Putative aldehydedehydrogenase-like protein YHR039C 0.000150213 3.06181E−05 4.906016788212 0.414872798 OS = Saccharomyces cerevisiae GN = MSC7 PE = 1 SV = 1Glucosamine--fructose-6-phosphate aminotransferase 0.0005219690.000109122 4.783366368 213 0.416829746 [isomerizing] OS = Saccharomycescerevisiae GN = GFA1 PE = 1 SV = 4 Uncharacterized GTP-binding proteinOLA1 OS = 0.001879535 0.000395467 4.752703763 214 0.418786693Saccharomyces cerevisiae GN = OLA1 PE = 1 SV = 1 Probable1-acyl-sn-glycerol-3-phosphate acyltransferase 0.000300341 6.44409E−054.660715949 215 0.42074364 OS = Saccharomyces cerevisiae GN = SLC1 PE =1 SV = 1 Sporulation-specific protein 21 OS = Saccharomyces 0.0001456443.12494E−05 4.660715949 216 0.422700587 cerevisiae GN = SPO21 PE = 1 SV= 1 Cell division control protein 42 OS = Saccharomyces 0.0004773290.000102415 4.660715949 216 0.422700587 cerevisiae GN = CDC42 PE = 1 SV= 2 Serine/threonine-protein phosphatase PP-Z2 OS = 0.0001296642.78207E−05 4.660715949 216 0.422700587 Saccharomyces cerevisiae GN =PPZ2 PE = 1 SV = 4 Putative mitochondrial carrier protein YHM1/SHM1 OS =Saccharomyces cerevisiae GN = YHM1 PE = 1 SV = 1 0.0003064 6.57409E−054.660715949 216 0.422700587 60S ribosomal protein L24-A OS =Saccharomyces 0.001155633 0.000247952 4.660715949 216 0.422700587cerevisiae GN = RPL24A PE = 1 SV = 1 60S ribosomal protein L35 OS =Saccharomyces 0.001463371 0.00031398 4.660715949 216 0.422700587cerevisiae GN = RPL35A PE = 1 SV = 1 Mitochondrial respiratory chaincomplexes assembly 0.000109111 2.34108E−05 4.660715949 222 0.43444227protein RCA1 OS = Saccharomyces cerevisiae GN = RCA1 PE = 1 SV = 2Prohibitin-1 OS = Saccharomyces cerevisiae GN = PHB1 0.0006476980.00013897 4.660715949 222 0.43444227 PE = 1 SV = 2 T-complex protein 1subunit epsilon OS = 0.000164381 3.52695E−05 4.660715949 222 0.43444227Saccharomyces cerevisiae GN = CCT5 PE = 1 SV = 3 Translationmachinery-associated protein 22 OS = 0.000452437 9.70746E−05 4.660715949222 0.43444227 Saccharomyces cerevisiae (strain YJM789) GN = TMA22 PE =3 SV = 1 DnaJ homolog 1, mitochondrial OS = Saccharomyces 0.0001831813.93031E−05 4.660715949 222 0.43444227 cerevisiae GN = MDJ1 PE = 1 SV =1 Alpha,alpha-trehalose-phosphate synthase [UDP- 0.000725072 0.0001555714.660715949 222 0.43444227 forming] 56 kDa subunit OS = Saccharomycescerevisiae GN = TPS1 PE = 1 SV = 2 Acetyl-coenzyme A synthetase 2 OS =Saccharomyces 0.001617845 0.000347124 4.660715949 222 0.43444227cerevisiae GN = ACS2 PE = 1 SV = 1 60S ribosomal protein L24-B OS =Saccharomyces 0.001159999 0.000248889 4.660715949 222 0.43444227cerevisiae GN = RPL24B PE = 1 SV = 1 Protein YGP1 OS = Saccharomycescerevisiae 0.00027266 5.85018E−05 4.660715949 222 0.43444227 GN = YGP1PE = 1 SV = 2 Actin-related protein 2/3 complex subunit 3 OS =0.000494562 0.000106113 4.660715949 231 0.452054795 Saccharomycescerevisiae GN = ARC18 PE = 1 SV = 1 Isoleucyl-tRNA synthetase,cytoplasmic OS = 0.001141147 0.000248582 4.590629995 232 0.454011742Saccharomyces cerevisiae GN = ILS1 PE = 1 SV = 1 Eukaryotic translationinitiation factor 3 subunit I 0.000511405 0.000112692 4.538065529 2330.455968689 OS = Saccharomyces cerevisiae (strain YJM789) GN = TIF34 PE= 3 SV = 1 Dolichol-phosphate mannosyltransferase OS = 0.0012878840.000287683 4.476740319 234 0.457925636 Saccharomyces cerevisiae GN =DPM1 PE = 1 SV = 3 40S ribosomal protein S29-B OS = Saccharomyces0.001433232 0.000324597 4.415415109 235 0.459882583 cerevisiae GN =RPS29B PE = 1 SV = 3 Pre-mRNA-splicing factor ATP-dependent RNA helicase0.000110115 2.49388E−05 4.415415109 236 0.46183953 PRP43 OS =Saccharomyces cerevisiae GN = PRP43 PE = 1 SV = 1 Translocation proteinSEC72 OS = Saccharomyces 0.000446225 0.000101061 4.415415109 2360.46183953 cerevisiae GN = SEC72 PE = 1 SV = 3 Transcription elongationfactor SPT5 OS = Saccharomyces 0.000166746 3.77645E−05 4.415415109 2360.46183953 cerevisiae GN = SPT5 PE = 1 SV = 1 Endoplasmic reticulumtransmembrane protein 1 OS = 0.000411557 9.32092E−05 4.415415109 2360.46183953 Saccharomyces cerevisiae GN = YET1 PE = 1 SV = 1Ferrochelatase,mitochondrial OS = Saccharomyces 0.000216204 4.89658E−054.415415109 236 0.46183953 cerevisiae GN = HEM15 PE = 1 SV = 1 ProteinCBP3, mitochondrial OS = Saccharomyces 0.000246696 5.58715E−054.415415109 236 0.46183953 cerevisiae GN = CBP3 PE = 1 SV = 1 Putativeprotein disulfide-isomerase YIL005W OS = Saccharomyces cerevisiae GN =YIL005W PE = 1 SV = 1 0.000118712 2.68857E−05 4.415415109 236 0.46183953Mitochondrial protein import protein MAS5 OS = 0.000863384 0.0001955394.415415109 236 0.46183953 Saccharomyces cerevisiae GN = YDJ1 PE = 1 SV= 1 Peroxisomal-coenzyme A synthetase 0.000159402 3.61013E−054.415415109 236 0.46183953 OS = Saccharomyces cerevisiae GN = FAT2 PE =1 SV = 1 Nuclear cap-binding protein complex subunit 1 OS = 0.0001927994.36651E−05 4.415415109 245 0.479452055 Saccharomyces cerevisiae GN =STO1 PE = 1 SV = 2 Proteasome component Y13 OS = Saccharomyces0.000335781 7.60474E−05 4.415415109 245 0.479452055 cerevisiae GN = PRE9PE = 1 SV = 1 Trehalose synthase complex regulatory subunit TSL 1 OS =0.000304804 7.10041E−05 4.29276469 247 0.483365949 Saccharomycescerevisiae GN = TSL1 PE = 1 SV = 1 Ribosomal RNA-processing protein 12OS = 6.62221E−05 1.58802E−05 4.17011427 248 0.485322896 Saccharomycescerevisiae GN = RRP12 PE = 1 SV = 1 U3 small nucleolar RNA-associatedprotein 22 OS = 6.48185E−05 1.55436E−05 4.17011427 248 0.485322896Saccharomyces cerevisiae GN = UTP22 PE = 1 SV = 1 40S ribosomal proteinS26-B OS = Saccharomyces 0.001354434 0.000324795 4.17011427 2480.485322896 cerevisiae GN = RPS26B PE = 1 SV = 1 Elongator complexprotein OS = Saccharomyces 5.95221E−05 1.42735E−05 4.17011427 2480.485322896 cerevisiae GN = IKI3 PE = 1 SV = 1 Probable1,3-beta-glucanosyltransferase GAS3 OS = 0.000160338 3.84492E−054.17011427 252 0.493150685 Saccharomyces cerevisiae GN = GAS3 PE = 1 SV= 1 Dynamin-related protein DNM1 OS = Saccharomyces 0.0004286610.000102794 4.17011427 252 0.493150685 cerevisiae GN = DNM1 PE = 1 SV =1 Pyruvate dehydrogenase complex protein X component, 0.0004014899.62777E−05 4.17011427 252 0.493150685 mitochondrial OS = Saccharomycescerevisiae GN = PDX1 PE = 1 SV = 1 GTP-binding protein RHO3 OS =Saccharomyces 0.00035976 8.6271E−05 4.17011427 252 0.493150685cerevisiae GN = RHO3 PE = 1 SV = 2 DNA-directed RNA polymerase I subunitRPA2 OS = 0.000130225 3.21744E−05 4.04746385 256 0.500978474Saccharomyces cerevisiae GN = RPA2 PE = 1 SV = 1 54S ribosomal proteinYmL6, mitochondrial OS = 0.000268086 6.83055E−05 3.92481343 2570.502935421 Saccharomyces cerevisiae GN = YML6 PE = 1 SV = 1 ER-derivedversicles protein ERV29 OS = Saccharomyces 0.000244777 6.23666E−053.92481343 257 0.502935421 cerevisiae GN = ERV29 PE = 1 SV = 1 54Sribosomal protein L3, mitochondrial OS = 0.000194787 4.96296E−053.92481343 257 0.502935421 Saccharomyces cerevisiae GN = MRPL3 PE = 1 SV= 2 Pyrroline-5-carboxylate reductase OS = Saccharomyces 0.0002844497.24746E−05 3.92481343 257 0.502935421 cerevisiae GN = PRO3 PE = 1 SV =1 60S ribosomal protein L34-A OS = Saccharomyces 0.000628399 0.0001601093.92481343 257 0.502935421 cerevisiae GN = RPL34A PE = 1 SV = 1Serine/threonine-protein kinase YPK1 OS = 0.000112061 2.85519E−053.92481343 257 0.502935421 Saccharomyces cerevisiae GN = YPK1 PE = 1 SV= 2 60S ribosomal protein L19 OS = Saccharomyces 0.000789773 0.0002012263.92481343 257 0.502935421 cerevisiae GN = RPL19A PE = 1 SV = 5CDP-diacylglycerol--inositol 3-phosphatidyltransferase 0.0003452618.79687E−05 3.92481343 264 0.516634051 OS = Saccharomyces cerevisiae GN= PIS1 PE = 1 SV = 1 60S ribosome subunit biogenesis protein NIP7 OS =0.00042053 0.000107146 3.92481343 264 0.516634051 Saccharomycescerevisiae GN = NIP7 PE = 1 SV = 1 Cell division control protein 10 OS =Saccharomyces 0.00023148 5.89787E−05 3.92481343 264 0.516634051cerevisiae GN = CDC10 PE = 1 SV = 1 E3 ubiquitin-protein ligase RSP5 OS= Saccharomyces 9.33468E−05 2.37837E−05 3.92481343 264 0.516634051cerevisiae GN = RSP5 PE = 1 SV = 1 Glucan 1,3-beta-glucosidase I/II OS =Saccharomyces 0.000167033 4.25582E−05 3.92481343 264 0.516634051cerevisiae GN = EXG1 PE = 1 SV = 1 Eukaryotic translation initiationfactor 5A-2 OS = 0.010829628 0.002807121 3.857913202 269 0.526418787Saccharomyces cerevisiae GN = HYP2 PE = 1 SV = 31,4-alpha-glucan-branching enzyme OS = Saccharomyces 0.0002047135.38413E−05 3.802163011 270 0.528375734 cerevisiae GN = GLC3 PE = 1 SV =2 Polyadenylate-binding protein, cytoplasmic and nuclear 0.0015234840.000407257 3.740837801 271 0.530332681 OS = Saccharomyces cerevisiae GN= PAB1 PE = 1 SV = 4 Protein GCY OS = Saccharomyces cerevisiae GN = GCY10.004153505 0.001120519 3.70676824 272 0.532289628 PE = 1 SV = 1Putative thiosulfate sulfurtransferase YOR285W OS = 0.0010426290.000283361 3.679512591 273 0.534246575 Saccharomyces cerevisiae GN =YOR285W PE = 1 SV = 1 DNA topoisomerase 2-associated protein PAT1 OS =9.07936E−05 2.46754E−05 3.679512591 274 0.536203523 Saccharomycescerevisiae GN = PAT1 PE = 1 SV = 3 CAAX prenyl protease 1 OS =Saccharomyces cerevisiae 0.000153556 4.17326E−05 3.679512591 2740.536203523 GN = STE24 PE = 1 SV = 1 Endoplasmic reticulum transmembraneprotein 3 OS = 0.000350817 9.53433E−05 3.679512591 274 0.536203523Saccharomyces cerevisiae GN = YET3 PE = 1 SV = 1 ATP-dependent RNAhelicase DOB1 OS = 6.58304E−05 1.78911E−05 3.679512591 277 0.542074364Saccharomyces cerevisiae GN = MTR4 PE = 1 SV = 1 Translationmachinery-associated protein 17 OS = 0.000479086 0.000130204 3.679512591277 0.542074364 Saccharomyces cerevisiae GN = TMA17 PE = 1 SV = 1 Carboncatabolite-derepressing protein kinase OS = 0.000111525 3.03099E−053.679512591 277 0.542074364 Saccharomyces cerevisiae GN = SNF1 PE = 1 SV= 1 tRNA (cytosine-5-)-methyltransferase NCL1 OS = 0.0001031742.80402E−05 3.679512591 277 0.542074364 Saccharomyces cerevisiae GN =NCL1 PE = 1 SV = 1 Protein transport protein SEC61 OS = Saccharomyces0.000151778 4.12496E−05 3.679512591 277 0.542074364 cerevisiae GN =SEC61 PE = 1 SV = 1 Calcineurin subunit B OS = Saccharomyces cerevisiae0.000409121 0.000111189 3.679512591 277 0.542074364 GN = CNB1 PE = 1 SV= 3 Lysophospholipase 1 OS = Saccharomyces cerevisiae 0.0001121143.04697E−05 3.679512591 277 0.542074364 GN = PLB1 PE = 1 SV = 2Proteasome component Y7 OS = Saccharomyces 0.000295812 8.03944E−053.679512591 277 0.542074364 cerevisiae GN = PRE8 PE = 1 SV = 1 Metalresistance protein YCF1 OS = Saccharomyces 4.69538E−05 1.27609E−053.679512591 277 0.542074364 cerevisiae GN = YCF1 PE = 1 SV = 2 RanGTPase-activating protein 1 OS = Saccharomyces 0.000175372 4.76619E−053.679512591 277 0.542074364 cerevisiae GN = RNA1 PE = 1 SV = 2L-aminoadipate-semialdehyde dehydrogenase OS = 0.000103446 2.81139E−053.679512591 277 0.542074364 Saccharomyces cerevisiae GN = LYS2 PE = 1 SV= 2 Serine hydroxymethyltransferase, mitochondrial OS = 0.0002993298.13501E−05 3.679512591 288 0.563600783 Saccharomyces cerevisiae GN =SHM1 PE = 1 SV = 2 Coatomer subunit alpha OS = Saccharomyces cerevisiae0.000351559 9.66186E−05 3.638629118 289 0.56555773 GN = RET1 PE = 1 SV =2 40S ribosomal protein S10-B OS = Saccharomyces 0.003742563 0.0010285643.638629118 289 0.56555773 cerevisiae GN = RPS10B PE = 1 SV = 1 40Sribosomal protein S10-A OS = Saccharomyces 0.003742269 0.0010284833.638629118 289 0.56555773 cerevisiae GN = RPS10A PE = 1 SV = 1Tryptophan synthase OS = Saccharomyces cerevisiae 0.0004124550.000113995 3.618187381 292 0.571428571 GN = TRP5 PE = 1 SV = 1Serine/threonine-protein phosphatase PP1-2 OS = 0.000865225 0.0002432553.556862171 293 0.573385519 Saccharomyces cerevisiae GN = GLC7 PE = 1 SV= 1 Aminopeptidase Y OS = Saccharomyces cerevisiae 0.0002583127.26236E−05 3.556862171 293 0.573385519 GN = APE3 PE = 1 SV = 1Glycerol-3-phosphate dehydrogenase [NAD+] 1 OS = 0.00143702 0.0004075273.526199566 295 0.577299413 Saccharomyces cerevisiae GN = GPD1 PE = 1 SV= 4 Valyl-tRNA synthetase, mitochondrial OS = 0.000732554 0.000208353.515978698 296 0.57925636 Saccharomyces cerevisiae GN = VAS1 PE = 1 SV= 2 Aconitate hydratase, mitochondrial OS = Saccharomyces 0.0043169720.001227815 3.515978698 297 0.581213307 cerevisiae GN = ACO1 PE = 1 SV =2 Elongation factor Tu, mitochondrial OS = Saccharomyces 0.0006364780.000182083 3.495536962 298 0.583170254 cerevisiae GN = TUF1 PE = 1 SV =1 Glycerol-3-phosphate O-acyltransferase 2 OS = 8.96548E−05 2.61064E−053.434211752 299 0.585127202 Saccharomyces cerevisiae GN = GPT2 PE = 1 SV= 1 Putative ribosomal RNA methyltransferase Nop2 OS = 0.0001074213.12796E−05 3.434211752 299 0.585127202 Saccharomyces cerevisiae GN =NOP2 PE = 1 SV = 1 Serine/threonine-protein kinase YPK2/YKR2 OS =9.78166E−05 2.8483E−05 3.434211752 299 0.585127202 Saccharomycescerevisiae GN = YPK2 PE = 1 SV = 1 Xanthine phosphoribosyltransferase 1OS = 0.000316809 9.22508E−05 3.434211752 302 0.590998043 Saccharomycescerevisiae GN = XPT1 PE = 1 SV = 1 3-hydroxy-3-methylglutaryl-coenzyme Areductase 2 OS = 6.48202E−05 1.88748E−05 3.434211752 302 0.590998043Saccharomyces cerevisiae GN = HMG2 PE = 1 SV = 1 3-keto-steroidreductase OS = Saccharomyces cerevisiae 0.000188778 5.49698E−053.434211752 302 0.590998043 GN = ERG27 PE = 1 SV = 1 Ras-like protein 2OS = Saccharomyces cerevisiae 0.000216093 6.29235E−05 3.434211752 3020.590998043 GN = RAS2 PE = 1 SV = 4 Protein phosphatase 1 regulatorysubunit SDS22 OS = 0.000192838 5.6152E−05 3.434211752 302 0.590998043Saccharomyces cerevisiae GN = SDS22 PE = 1 SV = 1 Ubiquitin-like proteinSMT3 OS = Saccharomyces 0.001293296 0.000376592 3.434211752 3020.590998043 cerevisiae GN = SMT3 PE = 1 SV = 1 Sphingosine-1-phosphatelyase OS = Saccharomyces 0.000114378 3.33055E−05 3.434211752 3020.590998043 cerevisiae GN = DPL1 PE = 1 SV = 1 Protein transport proteinSSS1 OS = Saccharomyces 0.000838514 0.000244165 3.434211752 3020.590998043 cerevisiae GN = SSS1 PE = 1 SV = 2 UPF0674 endoplasmicreticulum membrane protein 0.000159242 4.63692E−05 3.434211752 3020.590998043 YNR021 OS = Saccharomyces cerevisiae GN = YNR021W PE = 1 SV= 3 Non-classical export protein 2 OS = Saccharomyces 0.0003953830.000115131 3.434211752 302 0.590998043 cerevisiae GN = NCE102 PE = 1 SV= 1 Reduced viability upon starvation protein 161 OS = 0.0002479027.21859E−05 3.434211752 302 0.590998043 Saccharomyces cerevisiae GN =RVS161 PE = 1 SV = 1 Cytochrome b5 OS = Saccharomyces cerevisiae GN =0.000563995 0.000164228 3.434211752 302 0.590998043 CYB5 PE = 1 SV = 260S ribosomal protein L37-A OS = Saccharomyces 0.00076134 0.0002216933.434211752 302 0.590998043 cerevisiae GN = RPL37A PE = 1 SV = 2Calmodulin OS = Saccharomyces cerevisiae GN = CMD1 0.0004647830.000135339 3.434211752 302 0.590998043 PE = 1 SV = 1 Actin-relatedprotein 2/3 complex subunit 5 OS = 0.000437682 0.000127447 3.434211752302 0.590998043 Saccharomyces cerevisiae GN = ARC15 PE = 1 SV = 1Mitochondrial outer membrane protein SCY_3392 OS = 9.17107E−052.6705E−05 3.434211752 317 0.62035225 Saccharomyces cerevisiae (strainYJM789) GN = SCY_3392 PE = 3 SV = 1 tRNA pseudouridine synthase 1 OS =Saccharomyces 0.000120677 3.51396E−05 3.434211752 317 0.62035225cerevisiae GN = PUS1 PE = 1 SV = 1 Heterotrimeric G protein gammasubunit GPG1 OS = 0.00050257 0.000146342 3.434211752 317 0.62035225Saccharomyces cerevisiae GN = GPG1 PE = 1 SV = 1 Anthranilate synthasecomponent 1 OS = Saccharomyces 0.000132104 3.84672E−05 3.434211752 3200.626223092 cerevisiae GN = TRP2 PE = 1 SV = 4 UPF0662 protein YPL260WOS = Saccharomyces 0.000230371 6.95657E−05 3.311561332 321 0.628180039cerevisiae GN = YPL260W PE = 1 SV = 1 NADPH-dependent1-acyldihydroxyacetone phosphate 0.000440749 0.000133094 3.311561332 3210.628180039 reductase OS = Saccharomyces cerevisiae GN = AYR1 PE = 1 SV= 1 Long-chain-fatty-acid--CoA ligase 1 OS = Saccharomyces 0.0005572240.000168266 3.311561332 323 0.632093933 cerevisiae GN = FAA1 PE = 1 SV =1 Small COPII coat GTPase SAR1 OS = Saccharomyces 0.001323495 0.00040723.250236122 324 0.634050881 cerevisiae GN = SAR1 PE = 1 SV = 1 GMPsynthase [glutamine-hydrolyzing] OS = 0.000485453 0.0001493593.250236122 325 0.636007828 Saccharomyces cerevisiae GN = GUA1 PE = 1 SV= 4 Mitochondrial outer membrane protein porin 1 OS = 0.0032567250.001004705 3.241475378 326 0.637964775 Saccharomyces cerevisiae GN =POR1 PE = 1 SV = 4 ATP-dependent helicase NAM7 OS = Saccharomyces6.36357E−05 1.99553E−05 3.188910912 327 0.639921722 cerevisiae GN = NAM7PE = 1 SV = 1 Proteasome component PRE2 OS = Saccharomyces 0.0002201176.90258E−05 3.188910912 327 0.639921722 cerevisiae GN = PRE2 PE = 1 SV =3 Homocitrate synthase, mitochondrial OS = 0.000859811 0.0002696253.188910912 327 0.639921722 Saccharomyces cerevisiae GN = LYS21 PE = 1SV = 1 Nucleolar complex protein 2 OS = Saccharomyces 8.53356E−052.67601E−05 3.188910912 330 0.645792564 cerevisiae GN = NOC2 PE = 1 SV =2 Transcriptional regulatory protein SIN3 OS = 3.9829E−05 1.24898E−053.188910912 330 0.645792564 Saccharomyces cerevisiae GN = SIN3 PE = 1 SV= 2 Ribosome biogenesis protein ERB1 OS = 7.59361E−05 2.38126E−053.188910912 330 0.645792564 Saccharomyces cerevisiae (strain YJM789) GN= ERB1 PE = 3 SV = 1 Dihydroxy-acid dehydratase, mitochondrial OS =0.000664668 0.000208431 3.188910912 330 0.645792564 Saccharomycescerevisiae GN = ILV3 PE = 1 SV = 2 Uncharacterized protein YKL054C OS =Saccharomyces 8.29339E−05 2.6007E−05 3.188910912 330 0.645792564cerevisiae GN = YKL054C PE = 1 SV = 1 DNA-directed RNA polymerases I,II, and III subunit 0.000841244 0.000263803 3.188910912 330 0.645792564RPABC5 OS = Saccharomyces cerevisiae GN = RPB10 PE = 1 SV = 2Mitochondrial presequence protease OS = 0.000124148 3.89313E−053.188910912 330 0.645792564 Saccharomyces cerevisiae GN = CYM1 PE = 1 SV= 2 Amidophosphoribosyltransferase OS = Saccharomyces 0.0001227753.85005E−05 3.188910912 330 0.645792564 cerevisiae GN = ADE4 PE = 1 SV =2 Protein ERP1 OS = Saccharomyces cerevisiae 0.000281662 8.83256E−053.188910912 330 0.645792564 GN = ERP1 PE = 1 SV = 1 Hsp90 co-chaperoneHCH1 OS = Saccharomyces 0.000403775 0.000126618 3.188910912 3300.645792564 cerevisiae GN = HCH1 PE = 1 SV = 1 Acetyl-CoA carboxylase OS= Saccharomyces cerevisiae 0.001223872 0.00038379 3.188910912 3300.645792564 GN = FAS3 PE = 1 SV = 2 Mitochondrial outer membrane proteinIML2 OS = 8.43558E−05 2.64528E−05 3.188910912 330 0.645792564Saccharomyces cerevisiae (strain YJM789) GN = IML2 PE = 3 SV = 1Choline-phosphate cytidylyltransferase OS = 0.000140944 4.41982E−053.188910912 342 0.66927593 Saccharomyces cerevisiae GN = PCT1 PE = 1 SV= 2 Nucleosome assembly protein OS = Saccharomyces 0.0001454254.56032E−05 3.188910912 342 0.66927593 cerevisiae GN = NAP1 PE = 1 SV =2 THO complex subunit 2 OS = Saccharomyces cerevisiae 3.78591E−051.18721E−05 3.188910912 342 0.66927593 GN = THO2 PE = 1 SV = 1 Secsixty-one protein homolog OS = Saccharomyces 0.000130618 4.096E−053.188910812 342 0.66927593 cerevisiae GN = SSH1 PE = 1 SV = 1 Cytochromec heme lyase OS = Saccharomyces 0.000231505 7.25968E−05 3.188910912 3420.66927593 cerevisiae GN = CYC3 PE = 1 SV = 1 Prefolding subunit 4 OS =Saccharomyces cerevisiae 0.000458719 0.000143848 3.188910912 3420.66927593 GN = GIM3 PE = 1 SV = 1 Gamma-glutamyl phosphate reductase OS= 0.000139998 4.39016E−05 3.188910912 342 0.66927593 Saccharomycescerevisiae GN = PRO2 PE = 1 SV = 1 60S ribosomal protein L37-B OS =Saccharomyces 0.000705676 0.000221291 3.188910912 342 0.66927593cerevisiae GN = RPL37B PE = 1 SV = 2 UPF0368 protein YPL225W OS =Saccharomyces 0.000798365 0.000250357 3.188910912 342 0.66927593cerevisiae GN = YPL225W PE = 1 SV = 1Dolichyl-phosphate-mannose--protein 7.91626E−05 2.48243E−05 3.188910912351 0.686888454 mannosyltransferase 4 OS = Saccharomyces cerevisiae GN =PMT4 PE = 1 SV = 1 Increased sodium tolerance protein 2 OS =Saccharomyces 6.57534E−05 2.06194E−05 3.188910912 351 0.686888454cerevisiae GN = IST2 PE = 1 SV = 1 Glucokinase-1 OS = Saccharomycescerevisiae 0.002234448 0.000709793 3.148027439 353 0.690802348 GN = GLK1PE = 1 SV = 1 Suppressor protein STM1 OS = Saccharomyces 0.0036074550.001164851 3.096923097 354 0.692759295 cerevisiae GN = STM1 PE = 1 SV =3 Uridylate kinase OS = Saccharomyces cerevisiae 0.00028029 9.52198E−052.943610073 355 0.694716243 GN = URA6 PE = 1 SV = 1 Myosin light chainOS = Saccharomyces cerevisiae 0.00078176 0.000265579 2.943610073 3550.694716243 GN = MLC1 PE = 1 SV = 1 Glucose-repressible alcoholdehydrogenase 6.78771E−05 2.30591E−05 2.943610073 357 0.698630137transcriptional effector OS = Saccharomyces cerevisiae GN = CCR4 PE = 1SV = 1 54S ribosomal protein L1, mitochondrial OS = 0.0002073777.04501E−05 2.943610073 357 0.698630137 Saccharomyces cerevisiae GN =MRPL1 PE = 1 SV = 1 Nuclear polyadenylated RNA-binding protein 3 OS =7.10775E−05 2.41464E−05 2.943610073 357 0.698630137 Saccharomycescerevisiae GN = NAB3 PE = 1 SV = 1 Phosphoglycerate mutase 2 OS =Saccharomyces 0.000178191 6.05348E−05 2.943610073 357 0.698630137cerevisiae GN = GPM2 PE = 1 SV = 1 3′(2′),5′-bisphosphate nucleotidaseOS = Saccharomyces 0.000164191 5.57789E−05 2.943610073 357 0.698630137cerevisiae GN = HAL2 PE = 1 SV = 1 Protein SEY1 OS = Saccharomycescerevisiae (strain 7.18829E−05 2.442E−05 2.943610073 357 0.698630137AWRI1631) GN = SEY1 PE = 3 SV = 1 Thiamine metabolism regulatory proteinTHI3 OS = 9.40228E−05 3.19413E−05 2.943610073 357 0.698630137Saccharomyces cerevisiae GN = THI3 PE = 1 SV = 1 Alpha-mannosidase OS =Saccharomyces cerevisiae 0.000103261 3.50796E−05 2.943610073 3570.698630137 GN = AMS1 PE = 1 SV = 2 [NU+] prion formation protein 1 OS =Saccharomyces 4.78514E−05 1.6256E−05 2.943610073 357 0.698630137cerevisiae GN = NEW1 PE = 1 SV = 1 T-complex protein 1 subunit beta OS =Saccharomyces 0.000112369 3.81738E−05 2.943610073 357 0.698630137cerevisiae GN = CCT2 PE = 1 SV = 1 Putative zinc metalloproteinaseYIL108W OS = 8.30332E−05 2.8208E−05 2.943610073 357 0.698630137Saccharomyces cerevisiae GN = YIL108W PE = 1 SV = 1 Prefoldin subunit 5OS = Saccharomyces cerevisiae 0.000350187 0.000118965 2.943610073 3570.698630137 GN = GIM5 PE = 1 SV = 1 Probable glycosidase CRH2 OS =Saccharomyces 0.000128804 4.37573E−05 2.943610073 357 0.698630137cerevisiae GN = UTR2 PE = 1 SV = 3 Coatomer subunit epsilon OS =Saccharomyces 0.00019001 6.45499E−05 2.943610073 357 0.698630137cerevisiae GN = SEC28 PE = 1 SV = 2 26S proteasome regulatory subunitRPN13 OS = 0.000359064 0.000121981 2.943610073 357 0.698630137Saccharomyces cerevisiae GN = RPN13 PE = 1 SV = 1 40S ribosomal proteinS28-A OS = Saccharomyces 0.001693466 0.000575302 2.943610073 3570.698630137 cerevisiae GN = RPS28A PE = 1 SV = 1 D-3-phosphoglyceratedehydrogenase 1 OS = 0.000125564 4.26565E−05 2.943610073 357 0.698630137Saccharomyces cerevisiae GN = SER3 PE = 1 SV = 1 Adenylosuccinatesynthetase OS = Saccharomyces 0.000133142 4.52308E−05 2.943610073 3570.698630137 cerevisiae GN = ADE12 PE = 1 SV = 3 CTP synthase 2 OS =Saccharomyces cerevisiae (strain 9.96651E−05 3.38581E−05 2.943610073 3750.733855186 YJM789) GN = URA8 PE = 3 SV = 1 ATP-dependent RNA helicaseHAS1 OS = 0.000113331 3.85006E−05 2.943610073 375 0.733855186Saccharomyces cerevisiae GN = HAS1 PE = 1 SV = 1 Zinc finger proteinZPR1 OS = Saccharomyces cerevisiae 0.000116721 3.96523E−05 2.943610073375 0.733855186 GN = ZPR1 PE = 1 SV = 1 26S proteasome regulatorysubunit RPN3 OS = 0.00010638 3.61393E−05 2.943610073 375 0.733855186Saccharomyces cerevisiae GN = RPN3 PE = 1 SV = 4 Peroxisomal membraneprotein PMP27 OS = 0.000239176 8.12526E−05 2.943610073 375 0.733855186Saccharomyces cerevisiae GN = PEX11 PE = 1 SV = 2 Ribose-phosphatepyrophosphokinase 5 OS = 0.000120138 4.08132E−05 2.943610073 3750.733855186 Saccharomyces cerevisiae GN = PRS5 PE = 1 SV = 1 U6snRNA-associated Sm-like protein LSm6 OS = 0.00068399 0.0002323642.943610073 375 0.733855186 Saccharomyces cerevisiae (strain YJM789) GN= LSM6 PE = 3 SV = 1 Protein HMF1 OS = Saccharomyces cerevisiae0.00046226 0.000157038 2.943610073 375 0.733855186 GN = HMF1 PE = 1 SV =1 General negative regulator of transcription subunit 1 OS = 2.67455E−059.08595E−06 2.943610073 375 0.733855186 Saccharomyces cerevisiae GN =NOT1 PE = 1 SV = 2 Putative glucokinase-2 OS = Saccharomyces cerevisiae0.000881255 0.000312395 2.820959653 384 0.75146771 GN = EMI2 PE = 1 SV =1 26S protease regulatory subunit 4 homolog OS = 0.000252314 8.94425E−052.820959653 385 0.753424658 Saccharomyces cerevisiae GN = RPT2 PE = 1 SV= 3 Sphingolipid long chain base-responsive protein LSP1 0.0015899430.000573593 2.771899485 386 0.755381605 OS = Saccharomyces cerevisiae GN= LSP1 PE = 1 SV = 1 UPF0001 protein YBL036C OS = Saccharomyces0.000202322 7.4981E−05 2.698309233 387 0.757338552 cerevisiae GN =YBL036C PE = 1 SV = 1 Galactose/lactose metabolism regulatory proteinGAL80 0.000121933 4.51887E−05 2.698309233 388 0.759295499 OS =Saccharomyces cerevisiae GN = GAL80 PE = 1 SV = 2 U3 small nucleolarribonucleoprotein protein IMP3 OS = 0.000269233 9.97785E−05 2.698309233388 0.759295499 Saccharomyces cerevisiae GN = IMP3 PE = 1 SV = 1 U3small nucleolar RNA-associated protein 21 OS = 5.62287E−05 2.08385E−052.698309233 388 0.759295499 Saccharomyces cerevisiae GN = UTP21 PE = 1SV = 1 DNA polymerase alpha catalytic subunit A OS = 3.53233E−051.30909E−05 2.698309233 388 0.759295499 Saccharomyces cerevisiae GN =POL1 PE = 1 SV = 2 Probable glycerophosphodiester phosphodiesterase0.000158949 5.89071E−05 2.68309233 388 0.759295499 YPL206C OS =Saccharomyces cerevisiae GN = YPL206C PE = 1 SV = 1 Cytochrome c oxidaseassembly protein COX15 OS = 0.000107801 3.99514E−05 2.698309233 3880.759295499 Saccharomyces cerevisiae GN = COX15 PE = 1 SV = 1 U6snRNA-associated Sm-like protein LSm5 OS = 0.000565322 0.000209512.698309233 388 0.759295499 Saccharomyces cerevisiae GN = LSM5 PE = 1 SV= 1 60S ribosomal protein L29 OS = Saccharomyces 0.000883547 0.0003274452.698309233 388 0.759295499 cerevisiae GN = RPL29 PE = 1 SV = 3Tricalbin-3 OS = Saccharomyces cerevisiae GN = TCB3 6.88849E−052.55289E−05 2.698309233 388 0.759295499 PE = 1 SV = 1 Peroxiredoxin HYR1OS = Saccharomyces cerevisiae 0.000632164 0.000234282 2.698309233 3880.759295499 GN = HYR1 PE = 1 SV = 1 Glucose-6-phosphate 1-dehydrogenaseOS = 0.000409742 0.000151852 2.698309233 388 0.759295499 Saccharomycescerevisiae GN = ZWF1 PE = 1 SV = 4 Endosomal protein P24B OS =Saccharomyces 0.000252541 9.35923E−05 2.698309233 388 0.759295499cerevisiae GN = EMP24 PE = 1 SV = 1 Proteasome component C1 OS =Saccharomyces 0.000186846 6.92457E−05 2.698309233 388 0.759295499cerevisiae GN = PRE10 PE = 1 SV = 2 26S proteasome regulatory subunitRPN6 OS = 0.000118379 4.38716E−05 2.698309233 388 0.759295499Saccharomyces cerevisiae GN = RPN6 PE = 1 SV = 3 Monothiolglutaredoxin-3 OS = Saccharomyces cerevisiae 0.000181409 6.72305E−052.698309233 388 0.759295499 GN = GRX3 PE = 1 SV = 1 C-8 sterol isomeraseOS = Saccharomyces cerevisiae 0.000236677 8.77132E−05 2.698309233 3880.759295499 GN = ERG2 PE = 1 SV = 1 Uncharacterized membraneglycoprotein YNR065C OS = 4.70626E−05 1.74415E−05 2.698309233 3880.759295499 Saccharomyces cerevisiae GN = YNR065C PE = 1 SV = 1Ubiquitin carboxyl-terminal hydrolase 6 OS = 0.000103173 3.82361E−052.698309233 405 0.792563601 Saccharomyces cerevisiae GN = UBP6 PE = 1 SV= 1 Histone chaperone ASF1 OS = Saccharomyces 0.000186452 6.90996E−052.698309233 405 0.792563601 cerevisiae GN = ASF1 PE = 1 SV = 1 Pumiliohomology domain family member 6 OS = 0.000156904 5.81491E−05 2.698309233405 0.792563601 Saccharomyces cerevisiae GN = PUF6 PE = 1 SV = 1Mitochondrial outer membrane protein OM14 0.00040332 0.0001494712.698309233 405 0.792563601 OS = Saccharomyces cerevisiae (strainYJM789) GN = OM14 PE = 3 SV = 1 AP-1 complex subunit gamma-1 OS =Saccharomyces 6.29325E−05 2.33229E−05 2.698309233 405 0.792563601cerevisiae GN = APL4 PE = 1 SV = 1 Signal recognition particle subunitSRP72 OS = 8.01207E−05 2.96929E−05 2.698309233 405 0.792563601Saccharomyces cerevisiae GN = SRP72 PE = 1 SV = 2 Protein transportprotein SEC31 OS = Saccharomyces 4.24814E−05 1.57437E−05 2.698309233 4050.792563601 cerevisiae GN = SEC31 PE = 1 SV = 2 PhosphatidylethanolamineN-methyltransferase OS = 5.8221E−05 2.15769E−05 2.698309233 4050.792563601 Saccharomyces cerevisiae GN = PEM1 PE = 1 SV = 1Mitochondrial import inner membrane translocase 0.000363362 0.0001346632.698309233 405 0.792563601 subunit TIM16 OS = Saccharomyces cerevisiaeGN = PAM16 PE = 1 SV = 1 Phosphatidate cytidylyltransferase OS =Saccharomyces 0.000113698 4.21366E−05 2.698309233 405 0.792563601cerevisiae GN = CDS1 PE = 1 SV = 1 26S proteasome regulatory subunitRPN12 OS = 0.000184589 6.84093E−05 2.698309233 405 0.792563601Saccharomyces cerevisiae GN = RPN12 PE = 1 SV = 3 N-terminalacetyltransferase A complex subunit NAT1 5.95728E−05 2.20778E−052.698309233 405 0.792563601 OS = Saccharomyces cerevisiae GN = NAT1 PE =1 SV = 2 Nucleolar pre-ribosomal-associated protein 1 OS = 2.89842E−051.07416E−05 2.698309233 405 0.792563601 Saccharomyces cerevisiae GN =URB1 PE = 1 SV = 2 GU4 nucleic-binding protein 1 OS = Saccharomyces0.001107392 0.000415119 2.667646629 418 0.818003914 cerevisiae GN = ARC1PE = 1 SV = 2 Mitochondrial peculiar membrane protein 1 OS = 0.0008090290.000306801 2.636984024 419 0.819960861 Saccharomyces cerevisiae GN =MPM1 PE = 1 SV = 1 6-phosphogluconate dehydrogenase, decarboxylating 1OS = 0.00494208 0.001876038 2.63431771 420 0.821917808 Saccharomycescerevisiae GN = GND1 PE = 1 SV = 1 Transcription-associated protein 1 OS= Saccharomyces 2.59681E−05 1.00821E−05 2.575658814 421 0.823874755cerevisiae GN = TRA1 PE = 1 SV = 1 RNA polymerase-associated proteinCTR9 OS = 0.000180474 7.00692E−05 2.575658814 421 0.823874755Saccharomyces cerevisiae GN = CTR9 PE = 1 SV = 2 DNA-directed RNApolymerases I, II, and III subunit 0.000681273 0.000264504 2.575658814423 0.82778865 RPABC3 OS = Saccharomyces cerevisiae GN = RPB8 PE = 1 SV= 1 Ribonucleoside-diphosphate reductase large chain 1 OS = 0.0001129854.38663E−05 2.575658814 423 0.82778865 Saccharomyces cerevisiae GN =RNR1 PE = 1 SV = 2 60S ribosomal protein L10 OS = Saccharomyces0.003548365 0.001377653 2.575658814 423 0.82778865 cerevisiae GN = RPL10PE = 1 SV = 1 Sphingolipid long chain base-responsive protein PIL10.002318695 0.00091108 2.544996209 426 0.833659491 OS = Saccharomycescerevisiae GN = PIL1 PE = 1 SV = 1 Ribosome-associated complex subunitSSZ1 OS = 0.001333689 0.000524947 2.540615837 427 0.835616438Saccharomyces cerevisiae GN = SSZ1 PE = 1 SV = 2 Golgin IMH1 OS =Saccharomyces cerevisiae GN = IMH1 5.09048E−05 2.0752E−05 2.453008394428 0.837573386 PE = 1 SV = 1 Protein SCO2, mitochondrial OS =Saccharomyces 0.000153531 6.25888E−05 2.453008394 428 0.837573386cerevisiae GN = SCO2 PE = 1 SV = 1 3-ketoacyl-CoA reducatase OS =Saccharomyces 0.000138384 5.64138E−05 2.453008394 428 0.837573386cerevisiae GN = IFA38 PE = 1 SV = 1 Iron transport multicopper oxidaseFET5 OS = 7.55744E−05 3.08089E−05 2.453008394 428 0.837573386Saccharomyces cerevisiae GN = FET5 PE = 1 SV = 1 Protein ISD11 OS =Saccharomyces cerevisiae 0.000475466 0.00019383 2.453008394 4280.837573386 GN = ISD11 PE = 1 SV = 1 Mitochondrial distribution andmorphology protein 38 8.24018E−05 3.35921E−05 2.453008394 4280.837573386 OS = Saccharomyces cerevisiae GN = MDM38 PE = 1 SV = 1Elongation of fatty acids protein 3 OS = Saccharomyces 0.0001357285.53313E−05 2.453008394 428 0.837573386 cerevisiae GN = ELO3 PE = 1 SV =1 Nucleolar GTP-binding protein 1 OS = Saccharomyces 7.19874E−052.93466E−05 2.453008394 428 0.837573386 cerevisiae GN = NOG1 PE = 1 SV =1 Peptidyl-prolyl cis-trans isomerase ESS1 OS = 0.000276053 0.0001125372.453008394 428 0.837573386 Saccharomyces cerevisiae GN = ESS1 PE = 1 SV= 3 ATPase GET3 OS = Saccharomyces cerevisiae (strain 0.0001361145.54886E−05 2.453008394 428 0.837573386 RM11-1a) GN = GET3 PE = 3 SV = 1Protein APA1 OS = Saccharomyces cerevisiae GN = APA1 0.0001467855.98386E−05 2.453008394 428 0.837573386 PE = 1 SV = 4 Mitochondrialrespiratory chain complexes assembly 6.33584E−05 2.58288E−05 2.453008394439 0.859099804 protein AFG3 OS = Saccharomyces cerevisiae GN = AFG3 PE= 1 SV = 1 Calcium-transporting ATPase 2 OS = Saccharomyces 4.09332E−051.6687E−05 2.453008394 439 0.859099804 cerevisiae GN = PMC1 PE = 1 SV =1 Probable intramembrane protease YKL100C OS = 7.93266E−05 3.23385E−052.453008394 439 0.859099804 Saccharomyces cerevisiae GN = YKL100C PE = 1SV = 1 KH domain-containing protein YBL032W OS = 0.000128508 5.23877E−052.453008394 439 0.859099804 Saccharomyces cerevisiae GN = YBL032W PE = 1SV = 1 Mitochondrial import receptor subunit TOM22 OS = 0.0003190290.000130056 2.453008394 439 0.859099804 Saccharomyces cerevisiae GN =TOM22 PE = 1 SV = 3 Protein MSP1 OS = Saccharomyces cerevisiae0.00013277 5.41252E−05 2.453008394 439 0.859099804 GN = MSP1 PE = 1 SV =2 UPF0364 protein YMR027W OS = Saccharomyces 9.89598E−05 4.03422E−052.453008394 439 0.859099804 cerevisiae GN = YMR027W PE = 1 SV = 1Uncharacterized protein YJL217W OS = Saccharomyces 0.0002438589.94119E−05 2.453008394 439 0.859099804 cerevisiae GN = YJL217W PE = 1SV = 1 ER membrane protein complex subunit 4 OS = 0.0002496090.000101756 2.453008394 439 0.859099804 Saccharomyces cerevisiae GN =EMC4 PE = 1 SV = 1 Sm-like protein LSm1 OS = Saccharomyces cerevisiae0.000263782 0.000107534 2.453008394 439 0.859099804 GN = LSM1 PE = 1 SV= 1 Probable alpha-1,6-mannosyltransferase MNN10 OS = 0.0001145824.6711E−05 2.453008394 439 0.859099804 Saccharomyces cerevisiae GN =MNN10 PE = 1 SV = 1 Protein HAM1 OS = Saccharomyces cerevisiae0.000242455 9.884E−05 2.453008394 439 0.859099804 GN = HAM1 PE = 1 SV =1 NADPH-dependent methylglyoxal reductase GRE2 OS = 0.0001403395.7211E−05 2.453008394 439 0.859099804 Saccharomyces cerevisiae GN =GRE2 PE = 1 SV = 1 Alpha-1,2 mannosyltransferase KTR1 OS = 0.0001163924.74486E−05 2.453008394 439 0.859099804 Saccharomyces cerevisiae GN =KTR1 PE = 1 SV = 1 Protein VTH1 OS = Saccharomyces cerevisiae GN = VTH13.07094E−05 1.25191E−05 2.453008394 453 0.886497065 PE = 1 SV = 1Trehalose synthase complex regulatory subunit TPS3 OS = 4.50766E−051.8376E−05 2.453008394 453 0.886497065 Saccharomyces cerevisiae GN =TPS3 PE = 1 SV = 3 Heat shock protein 60, mitochondrial OS = 0.0065512670.002731813 2.398138469 455 0.890410959 Saccharomyces cerevisiae GN =HSP60 PE = 1 SV = 1 Pyruvate dehydrogenase E1 component subunit beta,0.001029786 0.000436161 2.361020579 456 0.892367906 mitochondrial OS =Saccharomyces cerevisiae GN = PDB1 PE = 1 SV = 2 Pyruvate dehydrogenaseE1 component subunit alpha, 0.00110963 0.000471203 2.354888058 4570.894324853 mitochondrial OS = Saccharomyces cerevisiae GN = PDA1 PE = 1SV = 2 Actin-related protein 3 OS = Saccharomyces cerevisiae 0.0002054378.81567E−05 2.330357974 458 0.8962818 GN = ARP3 PE = 1 SV = 1 AMPdeaminase OS = Saccharomyces cerevisiae GN = 0.000109083 4.68094E−052.330357974 458 0.8962818 AMD1 PE = 1 SV = 2 Lon protease homolog,mitochondrial OS = 0.000235988 0.000103075 2.289474501 460 0.900195695Saccharomyces cerevisiae GN = PIM1 PE = 1 SV = 2 Isocitratedehydrogenase [NAD] subunit 1, mitochondrial 0.003037645 0.0013327372.279253633 461 0.902152642 OS = Saccharomyces cerevisiae GN = IDH1 PE =1 SV = 2 Serine hydroxymethyltransferase, cytosolic OS = 0.0011283990.000501825 2.248591028 462 0.904109589 Saccharomyces cerevisiae GN =SHM2 PE = 1 SV = 2 Rab proteins geranylgeranyltransferase component A7.15564E−05 3.24121E−05 2.207707555 463 0.906066536 OS = Saccharomycescerevisiae GN = MRS6 PE = 1 SV = 2 37S ribosomal protein MRP1,mitochondrial OS = 0.000131255 5.9453E−05 2.207707555 463 0.906066536Saccharomyces cerevisiae GN = MRP1 PE = 1 SV = 2 Carboxypeptidase S OS =Saccharomyces cerevisiae 7.46309E−05 3.38047E−05 2.207707555 4630.906066536 GN = CPS1 PE = 1 SV = 2 Probable glucose transporter HXT5 OS= Saccharomyces 7.27682E−05 3.2961E−05 2.207707555 466 0.911937378cerevisiae GN = HXT5 PE = 1 SV = 1 Glycerol-3-phosphate dehydrogenase,mitochondrial OS = 0.000665985 0.000301664 2.207707555 466 0.911937378Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 Cytochrome b2,mitochondrial OS = Saccharomyces 7.35584E−05 3.33189E−05 2.207707555 4660.911937378 cerevisiae GN = CYB2 PE = 1 SV = 1 Translationmachinery-associated protein 20 OS = 0.000237747 0.00010769 2.207707555466 0.911937378 Saccharomyces cerevisiae GN = TMA20 PE = 1 SV = 1D-arabinono-1,4-lactone oxidase OS = Saccharomyces 8.10341E−053.67051E−05 2.207707555 466 0.911937378 cerevisiae GN = ALO1 PE = 1 SV =1 Protein phosphatase 2C homolog 3 OS = Saccharomyces 9.38112E−054.24926E−05 2.207707555 466 0.911937378 cerevisiae GN = PTC3 PE = 1 SV =3 DNA-directed RNA polymerase II subunit RPB9 OS = 0.0003374230.000152839 2.207707555 466 0.911937378 Saccharomyces cerevisiae GN =RPB9 PE = 1 SV = 1 Casein kinase II subunit alpha OS = Saccharomyces0.000107928 4.88868E−05 2.207707555 466 0.911937378 cerevisiae GN = CKA1PE = 1 SV = 1 26S protease regulatory subunit 6A OS = Saccharomyces9.99044E−05 4.52526E−05 2.207707555 466 0.911937378 cerevisiae GN = RPT5PE = 1 SV = 3 Enoyl reductase TSC13 OS = Saccharomyces cerevisiae0.000131115 5.93898E−05 2.207707555 466 0.911937378 GN = TSC13 PE = 1 SV= 1 H/ACA ribonucleoprotein complex subunit 2 OS = 0.0002815720.000127541 2.207707555 466 0.911937378 Saccharomyces cerevisiae GN =NHP2 PE = 1 SV = 1 Retrograde regulation protein 2 OS = Saccharomyces7.35221E−05 3.33024E−05 2.207707555 466 0.911937378 cerevisiae GN = RTG2PE = 1 SV = 2 Uncharacterized protein YDR476C OS = Saccharomyces0.000190809 8.64284E−05 2.207707555 466 0.911937378 cerevisiae GN =YDR476C PE = 1 SV = 1 DNA-directed RNA polymerases I and III subunitRPAC2 0.000298504 0.00013521 2.207707555 466 0.911937378 OS =Saccharomyces cerevisiae GN = RPC19 PE = 1 SV = 1 GPI transamidasecomponent GPI16 OS = 7.00996E−05 3.7522E−05 2.207707555 466 0.911937378Saccharomyces cerevisiae GN = GPI16 PE = 1 SV = 2 V-type proton ATPasesubunit e OS = Saccharomyces 0.000575236 0.000260558 2.207707555 4660.911937378 cerevisiae GN = VMA9 PE = 1 SV = 1 Cell division controlprotein 28 OS = Saccharomyces 0.000283067 0.000128217 2.207707555 4660.911937378 cerevisiae GN = CDC28 PE = 1 SV = 1 Serine/threonine-proteinphosphatase 2B catalytic 7.03504E−05 3.18658E−05 2.207707555 4660.911937378 subunit A2 OS = Saccharomyces cerevisiae GN = CNA2 PE = 1 SV= 2 GTP-binding protein YPT31/YPT8 OS = Saccharomyces 0.0001970228.92428E−05 2.207707555 466 0.911937378 cerevisiae GN = YPT31 PE = 1 SV= 3 FK506-binding nuclear protein OS = Saccharomyces 0.0001035594.69079E−05 2.207707555 466 0.911937378 cerevisiae GN = FPR3 PE = 1 SV =2 D-3-phosphoglycerate dehydrogenase 2 OS = 9.41815E−05 4.26603E−052.207707555 466 0.911937378 Saccharomyces cerevisiae GN = SER33 PE = 1SV = 1 Coatomer subunit beta OS = Saccharomyces cerevisiae 4.42208E−052.00302E−05 2.207707555 466 0.911937378 GN = SEC26 PE = 1 SV = 2Dipeptidyl aminopeptidase B OS = Saccharomyces 5.16141E−05 2.33791E−052.207707555 466 0.911937378 cerevisiae GN = DAP2 PE = 2 SV = 2 ProteinUTH1 OS = Saccharomyces cerevisiae (strain 0.000131237 5.94449E−052.207707555 466 0.911937378 RM11-1a) GN = UTH1 PE = 2 SV = 1Uncharacterized oxidoreductase YML125C OS = 0.000136619 6.18829E−052.207707555 490 0.95890411 Saccharomyces cerevisiae GN = YML125C PE = 1SV = 1 Long-chain-fatty-acid--CoA ligase 3 OS = Saccharomyces6.18498E−05 2.80154E−05 2.207707555 490 0.95890411 cerevisiae GN = FAA3PE = 1 SV = 1 Actin-related protein 2/3 complex subunit 2 OS =0.000243689 0.000110381 2.207707555 490 0.95890411 Saccharomycescerevisiae GN = ARC35 PE = 1 SV = 1 Ceramide very long chain fatty acidhydroxylase SCS7 0.000107415 4.86547E−05 2.207707555 490 0.95890411 OS =Saccharomyces cerevisiae GN = SCS7 PE = 1 SV = 1 Protein SDS24 OS =Saccharomyces cerevisiae (strain 8.43025E−05 3.81855E−05 2.207707555 4900.95890411 YJM789) GN = SDS24 PE = 3 SV = 1 Cytochrome c oxidaseassembly protein COX14 OS = 0.000605735 0.000274373 2.207707555 4900.95890411 Saccharomyces cerevisiae GN = COX14 PE = 1 SV = 1 Signalrecognition particle subunit SRP14 OS = 0.000293428 0.0001329112.207707555 490 0.95890411 Saccharomyces cerevisiae GN = SRP14 PE = 1 SV= 1 Putative guanine nucleotide-exchange factor SED4 OS = 4.22602E−051.91421E−05 2.207707555 497 0.97260274 Saccharomyces cerevisiae GN =SED4 PE = 1 SV = 1 Cytochrome b-c1 complex subunit 1, mitochondrial OS =0.000757196 0.000347809 2.17704495 498 0.974559687 Saccharomycescerevisiae GN = COR1 PE = 1 SV = 1 Lysyl-tRNA synthetase, cytoplasmic OS= 0.000693634 0.000321328 2.158647387 499 0.976516634 Saccharomycescerevisiae GN = KRS1 PE = 1 SV = 2 Glutamyl-tRNA synthetase, cytoplasmicOS = 0.00162997 0.000756317 2.155143089 500 0.978473581 Saccharomycescerevisiae GN = GUS1 PE = 1 SV = 3 Protein transport protein SEC13 OS =Saccharomyces 0.000567411 0.000264357 2.146382345 501 0.980430528cerevisiae GN = SEC13 PE = 1 SV = 1 Threonyl-tRNA synthetase,cytoplasmic OS = 0.000766861 0.00036171 2.120100112 502 0.982387476Saccharomyces cerevisiae GN = THS1 PE = 1 SV = 2 Uncharacterized proteinYMR178W OS = Saccharomyces 0.000877158 0.000420688 2.085057135 5030.984344423 cerevisiae GN = YMR178W PE = 1 SV = 1 40S ribosomal proteinS25-A OS = Saccharomyces 0.003025452 0.001451016 2.085057135 5030.984344423 cerevisiae GN = RPS25A PE = 1 SV = 1 Transposon Ty2-LR1Gag-Pol polyprotein OS = 4.50528E−05 2.16075E−05 2.085087135 5030.984344423 Saccharomyces cerevisiae GN = TY2B-LR1 PE = 3 SV = 1Farnesyl pyrophosphate synthase OS = Saccharomyces 0.0017862430.000863034 2.069725832 506 0.990215264 cerevisiae GN = FPP1 PE = 1 SV =2 Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial 0.0020353860.000989107 2.057801486 507 0.992172211 OS = Saccharomyces cerevisiae GN= IDH2 PE = 1 SV = 1 Nascent polypeptide-associated complex subunitbeta-1 0.001038594 0.000513207 2.023731925 508 0.994129159 OS =Saccharomyces cerevisiae (strain YJM789) GN = EGD1 PE = 3 SV = 1 40Sribosomal protein S3 OS = Saccharomyces 0.00598275 0.0029662832.016918013 509 0.996086106 cerevisiae GN = RPS3 PE = 1 SV = 5ATP-dependent RNA helicase SUB2 OS = 0.00052204 0.000260592 2.003290188510 0.998043053 Saccharomyces cerevisiae (strain YJM789) GN = SUB2 PE =3 SV = 1 Elongation factor 1-gamma 2 OS = Saccharomyces 0.0011284250.000563286 2.003290188 510 0.998043053 cerevisiae GN = TEF4 PE = 1 SV =1

TABLE 8Histone PTMs identified from GAL1 promoter chromatin isolated from cellsgrown in galactose-containing media. Protein Sequence Modifications PTMHistone H3 (R)EIAQDFkTDLR(F) Trimethyl (+42) K79me3 (R)EIAQDFkTDLR(F)Dimethyl (+28) K79me2 (R)EIAQDFkTDLR(F) Methyl (+14) K79me(R)FQkSTELLIR(K) Acetyl (+42) K56ac (R)KQLASkAAR(K) Acetyl (+42) K23ac(R)kQLASkAAR(K) Acetyl (+42), K18ac K23ac Acetyl (+42) (R)KSTGGkAPR(K)Acetyl (+42) K14ac (R)kSTGGkAPR(K) Acetyl (+42), K9ac K14ac Acetyl (+42)Histone H2B (K)AEkKPASkAPAEK(K) Acetyl (+42), K6ac K11ac Acetyl (+42)(K)KPASkAPAEKkPAAK(K) Acetyl (+42), K11ac K17ac Acetyl (+42)(K)APAEKkPAAK(K) Acetyl (+42) K17ac Histone H2A (K)GGkAGSAAK(A)Acetyl (+42) K7ac Histone H4 None Histone H3 Sequence Modifications PTMSpectrum ID (R)EIAQDFkTDLR(F) Trimethyl (+42) K79me3Tackett_051413_L1_21.3892.3892.3.dta (R)EIAQDFkTDLR(F) Trimethyl (+42)Tackett_051413_L1_19.3763.3763.2.dta (R)EIAQDFkTDLR(F) Dimethyl (+28)K79me2 Tackett_051413_L1_21.3948.3948.3.dta (R)EIAQDFkTDLR(F)Dimethyl (+28) Tackett_051413_L1_19.3877.3877.3.dta (R)EIAQDFkTDLR(F)Methyl (+14) K79me Tackett_051413_L1_19.3827.3827.3.dta(R)EIAQDFkTDLR(F) Acetyl (+42) K79acTackett_051413_L1_19.3776.3776.3.dta (R)EIAQDFkTDLR(F) Methyl (+14)Tackett_051413_L1_19.3815.3815.2.dta (R)EIAQDFkTDLR(F) Methyl (+14)Tackett_051413_L1_19.3832.3832.2.dta (R)FQkSTELLIR(K) Acetyl (+42) K56acTackett_051413_L1_20.5345.5345.2.dta (R)FQkSTELLIR(K) Acetyl (+42)Tackett_051413_L1_19.5128.5128.2.dta (R)FQkSTELLIR(K) Acetyl (+42)Tackett_051413_L1_19.5114.5114.2.dta (R)KQLASkAAR(K) Acetyl (+42) K23acTackett_051413_L1_16.1239.1239.2.dta (R)KQLASkAAR(K) Acetyl (+42)Tackett_051413_L1_01.1032.1032.2.dta (R)KQLASkAAR(K) Acetyl (+42)Tackett_051413_L1_20.1311.1311.2.dta (R)KQLASkAAR(K) Acetyl (+42)Tackett_051413_L1_20.1316.1316.2.dta (R)kQLASkAAR(K) Acetyl (+42), K18acTackett_051413_L1_19.2100.2100.2.dta Acetyl (+42) K23ac (R)KQLASkAAR(K)Acetyl (+42) Tackett_051413_L1_19.1327.1327.2.dta (R)KQLASkAAR(K)Acetyl (+42) Tackett_051413_L1_19.1340.1340.2.dta (R)kQLASkAAR(K)Acetyl (+42), Tackett_051413_L1_20.2166.2166.2.dta Acetyl (+42)(R)kQLASkAAR(K) Acetyl (+42), Tackett_051413_L1_20.2178.2178.2.dtaAcetyl (+42) (R)KSTGGkAPR(K) Acetyl (+42) K14acTackett_051413_L1_20.549.549.2.dta (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_23.698.698.2.dta (R)KSTGGkAPR(K) Acetyl (+42)Tackett_051413_L1_22.552.552.2.dta (R)kSTGGkAPR(K) Acetyl (+42), K9acTackett_051413_L1_12.1197.1197.2.dta Acetyl (+42) K14ac (R)KSTGGkAPR(K)Acetyl (+42) Tackett_051413_L1_19.506.506.2.dta (R)kSTGGkAPR(K)Acetyl (+42), Tackett_051413_L1_13.1112.1112.2.dta Acetyl (+42)(R)KSTGGkAPR(K) Acetyl (+42) Tackett_051413_L1_20.438.438.2.dta(R)KSTGGkAPR(K) Acetyl (+42) Tackett_051413_L1_22.555.555.2.dta(R)KSTGGkAPR(K) Acetyl (+42) Tackett_051413_L1_19.623.623.2.dta(R)KSTGGkAPR(K) Acetyl (+42) Tackett_051413_L1_19.627.627.2.dta(K)STGGkAPR(K) Acetyl (+42) Tackett_051413_L1_20.734.734.2.dta(K)STGGkAPR(K) Acetyl (+42) Tackett_051413_L1_19.715.715.2.dta(K)STGGkAPR(K) Acetyl (+42) Tackett_051413_L1_19.720.720.2.dta(K)STGGkAPR(K) Acetyl (+42) Tackett_051413_L1_20.744.744.2.dta(K)STELLIR(K) Tackett_051413_L1_16.3348.3348.2.dta (K)STELLIR(K)Tackett_051413_L1_19.3325.3325.2.dta (K)STELLIR(K)Tackett_051413_L1_20.3349.3349.2.dta

TABLE 9 Proteins enriched with CRISPR-ChAP-MS analysis of GAL1 promoterchromatin in galactose-containing media. Gene Accession gRNA/No gRNAsymbol Number MW (Fold Change) Identified Proteins (transcription)REB1_YEAST DNA-binding protein REB1 OS = Saccharomyces cerevisiae REB1P21538 92 kDa 8.1 GN = REB1 PE = 1 SV = 2 SPT5_YEAST Transcriptionelongation factor SPT5 OS = Saccharomyces SPT5 P27692 116 kDa  5.4cerevisiae GN = SPT5 PE = 1 SV = 1 TOA2_YEAST Transcription initiationfactor IIA small subunit TOA2 P32774 13 kDa 5.1 OS = Saccharomycescerevisiae GN = TOA2 PE = 1 SV = 1 BAF1_YEAST Transcription factor BAF1OS = Saccharomyces cerevisiae BAF1 P14164 82 kDa 4.7 GN = BAF1 PE = 1 SV= 3 SIN3_YEAST Transcriptional regulatory protein SIN3 OS =Saccharomyces SIN3 P22579 175 kDa  4.2 cerevisiae GN = SIN3 PE = 1 SV =2 H2B2_YEAST Histone H2B.2 OS = Saccharomyces cerevisiae GN = HTB2 PE =1 H2B2 P02294 14 kDa 4.1 SV = 2 UME1_YEAST Transcriptional regulatoryprotein UME1 OS = Saccharomyces UME1 Q03010 51 kDa 3.2 cerevisiae GN =UME1 PE = 1 SV = 1 POB3_YEAST FACT complex subunit POB3 OS =Saccharomyces cerevisiae POB3 Q04636 63 kDa 3 GN = POB3 PE = 1 SV = 1RSC6_YEAST Chromatin structure-remodeling complex protein RSC6 RSC6P25632 54 kDa 2.8 OS = Saccharomyces cerevisiae GN = RSC6 PE = 1 SV = 1RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14 RPA14 P50106 15kDa 2.4 OS = Saccharomyces cerevisiae GN = RPA14 PE = 1 SV = 1RSC7_YEAST Chromatin structure-remodeling complex subunit RSC7 RSC7P32832 50 kDa 2.1 OS = Saccharomyces cerevisiae GN = NPL6 PE = 1 SV = 1Identified Proteins (metabolic, ribosomal, common contaminants)PYRF_YEAST Orotidine 5′-phosphate decarboxylase OS = Saccharomyces PYRFP03962 29 kDa 15 cerevisiae GN = URA3 PE = 1 SV = 2 SCW4_YEAST Probablefamily 17 glucosidase SCW4 OS = Saccharomyces SCW4 P53334 40 kDa 15cerevisiae GN = SCW4 PE = 1 SV = 1 RAS2_YEAST Ras-like protein 2 OS =Saccharomyces cerevisiae GN = RAS2 RAS2 P01120 35 kDa 12 PE = 1 SV = 4PWP1_YEAST Periodic tryptophan protein 1 OS = Saccharomyces cerevisiaePWP1 P21304 64 kDa 11 GN = PWP1 PE = 1 SV = 1 ERG19_YEASTDiphosphomevalonate decarboxylase OS = Saccharomyces ERG19 P32377 44 kDa9.6 cerevisiae GN = ERG19 PE = 1 SV = 2 KEL1_YEAST Kelchrepeat-containing protein 1 OS = Saccharomyces cerevisiae KEL1 P38853131 kDa  9.6 GN = KEL1 PE = 1 SV = 1 BGL2_YEAST Glucan1,3-beta-glucosidase OS = Saccharomyces cerevisiae BGL2 P15703 34 kDa9.3 GN = BGL2 PE = 1 SV = 1 SCW10_YEAST Probable family 17 glucosidaseSCW10 OS = Saccharomyces SCW10 Q04951 40 kDa 7.2 cerevisiae GN = SCW10PE = 1 SV = 1 FKBP2_YEAST FK506-binding protein 2 OS = Saccharomycescerevisiae FKBP2 P32472 14 kDa 6 GN = FKB2 PE = 1 SV = 1 YKH7_YEASTUncharacterized protein YKL077W OS = Saccharomyces YKH7 P36081 46 kDa 6cerevisiae GN = YKL077W PE = 1 SV = 1 BRX1_YEAST Ribosome biogenesisprotein BRX1 OS = Saccharomyces BRX1 Q08235 34 kDa 5.8 cerevisiae GN =BRX1 PE = 1 SV = 1 PAL1_YEAST Uncharacterized protein YDR348C OS =Saccharomyces PAL1 Q05518 55 kDa 5.8 cerevisiae GN = YDR348C PE = 1 SV =1 KPR1_YEAST Ribose-phosphate pyrophosphokinase 1 OS = SaccharomycesKPR1 P32895 47 kDa 5 cerevisiae GN = PRS1 PE = 1 SV = 1 YM11_YEASTUncharacterized protein YMR124W OS = Saccharomyces YM11 P39523 106 kDa 5 cerevisiae GN = YMR124W PE = 1 SV = 2 PRS7_YEAST 26S proteaseregulatory subunit 7 homolog OS = Saccharomyces PRS7 P33299 52 kDa 5cerevisiae GN = RPT1 PE = 1 SV = 1 RRP9_YEAST Ribosomal RNA-processingprotein 9 OS = Saccharomyces RRP9 Q06506 65 kDa 5 cerevisiae GN = RRP9PE = 1 SV = 1 CIC1_YEAST Proteasome-interacting protein CIC1 OS =Saccharomyces CIC1 P38779 43 kDa 4.7 cerevisiae GN = CIC1 PE = 1 SV = 1MPM1_YEAST Mitochondrial peculiar membrane protein 1 OS = SaccharomycesMPM1 P40364 28 kDa 4 cerevisiae GN = MPM1 PE = 1 SV = 1 IDI1_YEASTIsopentenyl-diphosphate Delta-isomerase OS = Saccharomyces IDI1 P1549633 kDa 3.9 cerevisiae GN = IDI1 PE = 1 SV = 2 PEX14_YEAST Peroxisomalmembrane protein PEX14 OS = Saccharomyces PEX14 P53112 38 kDa 3.6cerevisiae GN = PEX14 PE = 1 SV = 1 YER0_YEAST Uncharacterized proteinYER080W OS = Saccharomyces YER0 P40053 72 kDa 3.5 cerevisiae GN =YER080W PE = 1 SV = 1 RT23_YEAST 37S ribosomal protein S23,mitochondrial OS = Saccharomyces RT23 Q01163 56 kDa 3.3 cerevisiae GN =RSM23 PE = 1 SV = 2 BUD21_YEAST Bud site selection protein 21 OS =Saccharomyces cerevisiae BUD21 Q08492 24 kDa 3.2 GN = BUD21 PE = 1 SV =1 ELOC_YEAST Elongin-C OS = Saccharomyces cerevisiae GN = ELC1 PE = 1ELOC Q03071 11 kDa 3.2 SV = 1 CDC11_YEAST Cell division control protein11 OS = Saccharomyces cerevisiae CDC11 P32458 48 kDa 3.1 GN = CDC11 PE =1 SV = 1 RFC2_YEAST Replication factor C subunit 2 OS = Saccharomycescerevisiae RFC2 P40348 40 kDa 3.1 GN = RFC2 PE = 1 SV = 1 EFTU_YEASTElongation factor Tu, mitochondrial OS = Saccharomyces EFTU P02992 48kDa 3 cerevisiae GN = TUF1 PE = 1 SV = 1 PPN1_YEAST EndopolyphosphataseOS = Saccharomyces cerevisiae PPN1 Q04119 78 kDa 3 GN = PPN1 PE = 1 SV =1 ETFA_YEAST Probable electron transfer flavoprotein subunit alpha, ETFAQ12480 37 kDa 3 mitochondrial OS = Saccharomyces cerevisiae GN = AIM45PE = 1 SV = 1 GBG_YEAST Guanine nucleotide-binding protein subunit gammaGBG P18852 13 kDa 3 OS = Saccharomyces cerevisiae GN = STE18 PE = 1 SV =1 PUR4_YEAST Phosphoribosylformylglycinamidine synthase PUR4 P38972 149kDa 3 OS = Saccharomyces cerevisiae GN = ADE6 PE = 1 SV = 2 SUCB_YEASTSuccinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial SUCBP53312 47 kDa 2.9 OS = Saccharomyces cerevisiae GN = LSC2 PE = 1 SV = 1UTP15_YEAST U3 small nucleolar RNA-associated protein 15 UTP15 Q04305 58kDa 2.9 OS = Saccharomyces cerevisiae GN = UTP15 PE = 1 SV = 1SEC3_YEAST Exocyst complex component SEC3 OS = Saccharomyces SEC3 P33332155 kDa  2.9 cerevisiae GN = SEC3 PE = 1 SV = 1 AML1_YEASTN(6)-adenine-specific DNA methyltransferase-like 1 AML1 P53200 29 kDa2.9 OS = Saccharomyces cerevisiae GN = AML1 PE = 1 SV = 2 RM10_YEAST 54Sribosomal protein L10, mitochondrial OS = Saccharomyces RM10 P36520 36kDa 2.9 cerevisiae GN = MRPL10 PE = 1 SV = 2 UCRI_YEAST Cytochrome b-c1complex subunit Rieske, mitochondrial UCRI P08067 23 kDa 2.8 OS =Saccharomyces cerevisiae GN = RIP1 PE = 1 SV = 1 KHSE_YEAST Homoserinekinase OS = Saccharomyces cerevisiae GN = THR1 KHSE P17423 39 kDa 2.8 PE= 1 SV = 4 SMD1_YEAST Small nuclear ribonucleoprotein Sm D1 OS =Saccharomyces SMD1 Q02260 16 kDa 2.8 cerevisiae GN = SMD1 PE = 1 SV = 1CYC1_YEAST Cytochrome c iso-1 OS = Saccharomyces cerevisiae GN = CYC1CYC1 P00044 12 kDa 2.6 PE = 1 SV = 2 PET10_YEAST Protein PET10 OS =Saccharomyces cerevisiae GN = PET10 PET10 P36139 31 kDa 2.6 PE = 1 SV =3 RT35_YEAST 37S ribosomal protein S35, mitochondrial OS = SaccharomycesRT35 P53292 40 kDa 2.6 cerevisiae GN = MRPS35 PE = 1 SV = 1 PROF_YEASTProfilin OS = Saccharomyces cerevisiae GN = PFY1 PE = 1 SV = 2 PROFP07274 14 kDa 2.6 NOP13_YEAST Nucleolar protein 13 OS = Saccharomycescerevisiae NOP13 P53883 46 kDa 2.6 GN = NOP13 PE = 1 SV = 1 RM27_YEAST54S ribosomal protein L27, mitochondrial OS = Saccharomyces RM27 P3652616 kDa 2.6 cerevisiae GN = MRPL27 PE = 1 SV = 2 YHA8_YEASTUncharacterized transporter YHL008C OS = Saccharomyces YHA8 P38750 70kDa 2.6 cerevisiae GN = YHL008C PE = 1 SV = 1 DYL1_YEAST Dynein lightchain 1, cytoplasmic OS = Saccharomyces cerevisiae DYL1 Q02647 10 kDa2.5 GN = DYN2 PE = 1 SV = 1 CDC73_YEAST Cell division control protein 73OS = Saccharomyces cerevisiae CDC73 Q06697 44 kDa 2.5 GN = CDC73 PE = 1SV = 1 HRB1_YEAST Protein HRB1 OS = Saccharomyces cerevisiae GN = HRB1PE = 1 HRB1 P38922 52 kDa 2.5 SV = 2 SNZ1_YEAST Pyridoxine biosynthesisprotein SNZ1 OS = Saccharomyces SNZ1 Q03148 32 kDa 2.5 cerevisiae GN =SNZ1 PE = 1 SV = 1 RS9A_YEAST 40S ribosomal protein S9-A OS =Saccharomyces cerevisiae RS9A O13516 22 kDa 2.4 GN = RPS9A PE = 1 SV = 3ARPC2_YEAST Actin-related protein 2/3 complex subunit 2 ARPC2 P53731 40kDa 2.4 OS = Saccharomyces cerevisiae GN = ARC35 PE = 1 SV = 1TRS31_YEAST Transport protein particle 31 kDa subunit OS = SaccharomycesTRS31 Q03337 32 kDa 2.4 cerevisiae GN = TRS31 PE = 1 SV = 1 PUT2_YEASTDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial PUT2 P0727564 kDa 2.4 OS = Saccharomyces cerevisiae GN = PUT2 PE = 1 SV = 2RM51_YEAST 54S ribosomal protein L51, mitochondrial OS = SaccharomycesRM51 Q06090 16 kDa 2.4 cerevisiae GN = MRPL51 PE = 1 SV = 1 LGUL_YEASTLactoylglutathione lyase OS = Saccharomyces cerevisiae LGUL P50107 37kDa 2.4 GN = GLO1 PE = 1 SV = 1 HIS8_YEAST Histidinol-phosphateaminotransferase OS = Saccharomyces HIS8 P07172 43 kDa 2.3 cerevisiae GN= HIS5 PE = 1 SV = 2 NPT1_YEAST Nicotinate phosphoribosyltransferase OS= Saccharomyces NPT1 P39683 49 kDa 2.3 cerevisiae GN = NPT1 PE = 1 SV =3 METK2_YEAST S-adenosylmethionine synthase 2 OS = Saccharomyces METK2P19358 42 kDa 2.2 cerevisiae GN = SAM2 PE = 1 SV = 3 FMP10_YEASTUncharacterized mitochondrial membrane protein FMP10 FMP10 P40098 28 kDa2.2 OS = Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 YPT31_YEASTGTP-binding protein YPT31/YPT8 OS = Saccharomyces YPT31 P38555 24 kDa2.2 cerevisiae GN = YPT31 PE = 1 SV = 3 (+1) YMX6_YEAST Uncharacterizedprotein YMR086W OS = Saccharomyces YMX6 Q04279 106 kDa 2.2 cerevisiae GN= YMR086W PE = 1 SV = 1 ACPM_YEAST Acyl carrier protein, mitochondrialOS = Saccharomyces ACPM P32463 14 kDa 2.2 cerevisiae GN = ACP1 PE = 1 SV= 1 RM33_YEAST 54S ribosomal protein L33, mitochondrial OS =Saccharomyces RM33 P20084 10 kDa 2.2 cerevisiae GN = MRPL33 PE = 1 SV =4 RL14A_YEAST 60S ribosomal protein L14-A OS = Saccharomyces cerevisiaeRL14A P36105 15 kDa 2.1 GN = RPL14A PE = 1 SV = 1 PBP1_YEASTPAB1-binding protein 1 OS = Saccharomyces cerevisiae PBP1 P53297 79 kDa2.1 GN = PBP1 PE = 1 SV = 1 GPDM_YEAST Glycerol-3-phosphatedehydrogenase, mitochondrial GPDM P32191 72 kDa 2.1 OS = Saccharomycescerevisiae GN = GUT2 PE = 1 SV = 2 RIB1_YEAST GTP cyclohydrolase-2 OS =Saccharomyces cerevisiae GN = RIB1 RIB1 P38066 38 kDa 2.1 PE = 1 SV = 2OTC_YEAST Ornithine carbamoyltransferase OS = Saccharomyces cerevisiaeOTC P05150 38 kDa 2.1 GN = ARG3 PE = 1 SV = 1 UBP6_YEAST Ubiquitincarboxyl-terminal hydrolase 6 OS = Saccharomyces UBP6 P43593 57 kDa 2.1cerevisiae GN = UBP6 PE = 1 SV = 1 SUR7_YEAST Protein SUR7 OS =Saccharomyces cerevisiae GN = SUR7 PE = 1 SUR7 P54003 34 kDa 2.1 SV = 1TWF1_YEAST Twinfilin-1 OS = Saccharomyces cerevisiae GN = TWF1 PE = 1TWF1 P53250 37 kDa 2.1 SV = 1 RN49_YEAST 54S ribosomal protein L49,mitochondrial OS = Saccharomyces RN49 P40858 18 kDa 2.1 cerevisiae GN =MRPL49 PE = 1 SV = 2 RSM28_YEAST 37S ribosomal protein RSM28,mitochondrial RSM28 Q03430 41 kDa 2.1 OS = Saccharomyces cerevisiae GN =RSM28 PE = 1 SV = 2 1832 protiens were identified and thoseenriched >2-fold (with at least 5 spectral counts) with Cas9-PrA/gRNAverses the no gRNA control are listed (86 proteins). Enrichment wascalculated by normalized NSAF as detailed in Byrum et al., 2013.Protiens are categorized as those involved in transcription (11proteins) and those that are common contaminants (74 proteins) inaffinity purifications (Byrum et al., 2013).

TABLE 10 Spectral counts and normalized NSAF values. gRNA/ Spectral nocounts Normalized gRNA Gene Accession No NSAF values (Fold IdentifiedProteins (318) Symbol Number MW gRNA gRNA gRNA No gRNA Change)PYRF_YEAST Orotidine 5′-phosphate PYRF P03962 29 657 45 2.3034 0.1557415 decarboxylase OS = Saccharomyces kDa cerevisiae GN = URA3 PE = 1 SV =2 SCW4_YEAST Probable family 17 SCW4 P53334 40 43 3 0.11355 0.0076196 15glucosidase SCW4 OS = Saccharomyces kDa cerevisiae GN = SCW4 PE = 1 SV =1 RAS2_YEAST Ras-like protein 2 RAS2 P01120 35 10 1 0.030093 0.002535812 OS = Saccharomyces cerevisiae kDa GN = RAS2 PE = 1 SV = 4 PWP1_YEASTPeriodic tryptophan PWP1 P21304 64 10 1 0.02054 0.0019358 11 protein 1OS = Saccharomyces kDa cerevisiae GN = PWP1 PE = 1 SV = 1 ERG19_YEASTDiphosphomevalonate ERG19 P32377 44 9 1 0.022174 0.0023133 9.6decarboxylase OS = Saccharomyces kDa cerevisiae GN = ERG19 PE = 1 SV = 2KEL1_YEAST Kelch repeat-containing KEL1 P38853 131 6 1 0.0054930.00057277 9.6 protein 1 OS = Saccharomyces kDa cerevisiae GN = KEL1 PE= 1 SV = 1 BGL2_YEAST Glucan 1,3-beta- BGL2 P15703 34 78 10 0.238540.02567 9.3 glucosidase OS = Saccharomyces kDa cerevisiae GN = BGL2 PE =1 SV = 1 REB1_YEAST DNA-binding protein REB1 P21538 92 5 1 0.0067680.00083919 8.1 REB1 OS = Saccharomyces cerevisiae kDa GN = REB1 PE = 1SV = 2 SCW10_YEAST Probable family 17 SCW10 Q04951 40 24 3 0.0673080.0093606 7.2 glucosidase SCW10 OS = Saccharomyces kDa cerevisiae GN =SCW10 PE = 1 SV = 1 FKBP2_YEAST FK506-binding protein 2 FKBP2 P32472 145 1 0.028788 0.0047652 6 OS = Saccharomyces cerevisiae kDa GN = FKB2 PE= 1 SV = 1 YKH7_YEAST Uncharacterized protein YKH7 P36081 46 5 10.010224 0.0017008 6 YKL077W OS = Saccharomyces kDa cerevisiae GN =YKL077W PE = 1 SV = 1 BRX1_YEAST Ribosome biogenesis BRX1 Q08235 34 10 20.032329 0.0055678 5.8 protein BRX1 OS = Saccharomyces kDa cerevisiae GN= BRX1 PE = 1 SV = 1 PAL1_YEAST Uncharacterized protein PAL1 Q05518 55 51 0.010082 0.0017505 5.8 YDR348C OS = Saccharomyces kDa cerevisiae GN =YDR348C PE = 1 SV = 1 SPT5_YEAST Transcription elongation SPT5 P27692116 5 1 0.005671 0.001046 5.4 factor SPT5 OS = Saccharomyces kDacerevisiae GN = SPT5 PE = 1 SV = 1 TOA2_YEAST Transcription initiationTOA2 P32774 13 5 1 0.026691 0.005273 5.1 factor IIA small subunit kDa OS= Saccharomyces cerevisiae GN = TOA2 PE = 1 SV = 1 KPR1_YEASTRibose-phosphate KPR1 P32895 47 8 2 0.020962 0.004191 5pyrophosphokinase 1 kDa OS = Saccharomyces cerevisiae GN = PRS1 PE = 1SV = 1 YM11_YEAST Uncharacterized protein YM11 P39523 106 6 2 0.0070740.001414 5 YMR124W OS = Saccharomyces kDa cerevisiae GN = YMR124W PE = 1SV = 2 PRS7_YEAST 26S protease regulatory PRS7 P33299 52 5 1 0.0111320.0022086 5 subunit 7 homolog OS = Saccharomyces kDa cerevisiae GN =RPT1 PE = 1 SV = 1 RRP9_YEAST Ribosomal RNA- RRP9 Q06506 65 5 1 0.010060.0020314 5 processing protein 9 OS = Saccharomyces kDa cerevisiae GN =RRP9 PE = 1 SV = 1 CIC1_YEAST Proteasome-interacting CIC1 P38779 43 6 10.014793 0.0031713 4.7 protein CIC1 OS = Saccharomyces kDa cerevisiae GN= CIC1 PE = 1 SV = 1 BAF1_YEAST Transcription factor BAF1 P14164 82 5 10.00721 0.0015254 4.7 BAF1 OS = Saccharomyces cerevisiae kDa GN = BAF1PE = 1 SV = 3 SIN3_YEAST Transcriptional SIN3 P22579 175 5 1 0.0037570.00088897 4.2 regulatory protein SIN3 kDa OS = Saccharomyces cerevisiaeGN = SIN3 PE = 1 SV = 2 H2B2_YEAST Histone H2B.2 H2B2 P02294 14 81 870.021748 0.0053125 4.1 OS = Saccharomyces cerevisiae kDa GN = HTB2 PE =1 SV = 2 MPM1_YEAST Mitochondrial peculiar MPM1 P40364 28 10 3 0.035950.0090786 4 membrane protein 1 OS = Saccharomyces kDa cerevisiae GN =MPM1 PE = 1 SV = 1 IDI1_YEAST Isopentenyl-diphosphate IDI1 P15496 33 185 0.054499 0.014115 3.9 Delta-isomerase OS = Saccharomyces kDacerevisiae GN = IDI1 PE = 1 SV = 2 PEX14_YEAST Peroxisomal PEX14 P5311238 11 3 0.032705 0.0090831 3.6 membrane protein PEX14 kDa OS =Saccharomyces cerevisiae GN = PEX14 PE = 1 SV = 1 YER0_YEASTUncharacterized protein YER0 P40053 72 11 3 0.018477 0.0052646 3.5YER080W OS = Saccharomyces kDa cerevisiae GN = YER080W PE = 1 SV = 1RT23_YEAST 37S ribosomal protein RT23 Q01163 56 5 2 0.010978 0.00332693.3 S23, mitochondrial OS = Saccharomyces kDa cerevisiae GN = RSM23 PE =1 SV = 2 BUD21_YEAST Bud site selection BUD21 Q08492 24 6 2 0.0232790.0073049 3.2 protein 21 OS = Saccharomyces kDa cerevisiae GN = BUD21 PE= 1 SV = 1 UME1_YEAST Transcriptional UME1 Q03010 51 6 2 0.0148750.0046531 3.2 regulatory protein UME1 kDa OS = Saccharomyces cerevisiaeGN = UME1 PE = 1 SV = 1 ELOC_YEAST Elongin-C ELOC Q03071 11 5 2 0.0414490.012996 3.2 OS = Saccharomyces cerevisiae kDa GN = ELC1 PE = 1 SV = 1CDC11_YEAST Cell division control CDC11 P32458 48 12 4 0.033015 0.0105093.1 protein 11 OS = Saccharomyces kDa cerevisiae GN = CDC11 PE = 1 SV =1 RFC2_YEAST Replication factor C RFC2 P40348 40 6 2 0.014126 0.00462623.1 subunit 2 OS = Saccharomyces kDa cerevisiae GN = RFC2 PE = 1 SV = 1EFTU_YEAST Elongation factor Tu, EFTU P02992 48 40 14 0.095198 0.0321 3mitochondrial OS = Saccharomyces kDa cerevisiae GN = TUF1 PE = 1 SV = 1PPN1_YEAST Endopolyphosphatase PPN1 Q04119 78 14 5 0.017319 0.0058652 3OS = Saccharomyces cerevisiae kDa GN = PPN1 PE = 1 SV = 1 POB3_YEASTFACT complex subunit POB3 Q04636 63 12 4 0.024482 0.0082034 3 POB3 OS =Saccharomyces cerevisiae kDa GN = POB3 PE = 1 SV = 1 ETFA_YEAST Probableelectron ETFA Q12480 37 11 4 0.027632 0.009349 3 transfer flavoproteinsubunit alpha, kDa mitochondrial OS = Saccharomyces cerevisiae GN =AIM45 PE = 1 SV = 1 GBG_YEAST Guanine nucleotide- GBG P18852 13 5 20.035393 0.011696 3 binding protein subunit gamma kDa OS = Saccharomycescerevisiae GN = STE18 PE = 1 SV = 1 PUR4_YEAST PUR4 P38972 149 5 20.004221 0.0014279 3 Phosphoribosylformylglycinamidine kDa synthase OS =Saccharomyces cerevisiae GN = ADE6 PE = 1 SV = 2 SUCB_YEAST Succinyl-CoAligase SUCB P53312 47 27 10 0.059446 0.020597 2.9 [ADP-forming] subunitbeta, kDa mitochondrial OS = Saccharomyces cerevisiae GN = LSC2 PE = 1SV = 1 UTP15_YEAST U3 small nucleolar UTP15 Q04305 58 8 3 0.018180.0063459 2.9 RNA-associated protein 15 kDa OS = Saccharomycescerevisiae GN = UTP15 PE = 1 SV = 1 SEC3_YEAST Exocyst complex SEC3P33332 155 7 3 0.006023 0.0020559 2.9 component SEC3 OS = SaccharomyceskDa cerevisiae GN = SEC3 PE = 1 SV = 1 AML1_YEAST N(6)-adenine-specificAML1 P53200 29 5 2 0.017364 0.006086 2.9 DNA methyltransferase-like 1kDa OS = Saccharomyces cerevisiae GN = AML1 PE = 1 SV = 2 RM10_YEAST 54Sribosomal protein RM10 P36520 36 5 2 0.013874 0.0047367 2.9 L10,mitochondrial OS = Saccharomyces kDa cerevisiae GN = MRPL10 PE = 1 SV =2 UCRI_YEAST Cytochrome b-c1 UCRI P08067 23 18 7 0.068993 0.024609 2.8complex subunit Rieske, mitochondrial kDa OS = Saccharomyces cerevisiaeGN = RIP1 PE = 1 SV = 1 KHSE_YEAST Homoserine kinase KHSE P17423 39 9 30.019995 0.0071271 2.8 OS = Saccharomyces cerevisiae kDa GN = THR1 PE =1 SV = 4 SMD1_YEAST Small nuclear SMD1 Q02260 16 8 3 0.040301 0.0143 2.8ribonucleoprotein Sm D1 kDa OS = Saccharomyces cerevisiae GN = SMD1 PE =1 SV = 1 RSC6_YEAST Chromatin structure- RSC6 P25632 54 7 3 0.0158750.00569 2.8 remodeling complex protein RSC6 kDa OS = Saccharomycescerevisiae GN = RSC6 PE = 1 SV = 1 CYC1_YEAST Cytochrome c iso-1 CYC1P00044 12 117 68 0.61144 0.2352 2.6 OS = Saccharomyces cerevisiae kDa GN= CYC1 PE = 1 SV = 2 PET10_YEAST Protein PET10 PET10 P36139 31 17 70.048927 0.019041 2.6 OS = Saccharomyces cerevisiae kDa GN = PET10 PE =1 SV = 3 RT35_YEAST 37S ribosomal protein RT35 P53292 40 12 5 0.0317110.011999 2.6 S35, mitochondrial OS = Saccharomyces kDa cerevisiae GN =MRPS35 PE = 1 SV = 1 PROF_YEAST Profilin PROF P07274 14 11 4 0.0588740.023044 2.6 OS = Saccharomyces cerevisiae kDa GN = PFY1 PE = 1 SV = 2NOP13_YEAST Nucleolar protein 13 NOP13 P53883 46 6 3 0.017094 0.00650242.6 OS = Saccharomyces cerevisiae kDa GN = NOP13 PE = 1 SV = 1RM27_YEAST 54S ribosomal protein RM27 P36526 16 5 2 0.024505 0.00953352.6 L27, mitochondrial OS = Saccharomyces kDa cerevisiae GN = MRPL27 PE= 1 SV = 2 YHA8_YEAST Uncharacterized YHA8 P38750 70 5 2 0.0093660.0036348 2.6 transporter YHL008C kDa OS = Saccharomyces cerevisiae GN =YHL008C PE = 1 SV = 1 DYL1_YEAST Dynein light chain 1, DYL1 Q02647 10 104 0.073508 0.029371 2.5 cytoplasmic OS = Saccharomyces kDa cerevisiae GN= DYN2 PE = 1 SV = 1 CDC73_YEAST Cell division control CDC73 Q06697 44 94 0.018285 0.0073158 2.5 protein 73 OS = Saccharomyces kDa cerevisiae GN= CDC73 PE = 1 SV = 1 HRB1_YEAST Protein HRB1 HRB1 P38922 52 9 40.020922 0.0084023 2.5 OS = Saccharomyces cerevisiae kDa GN = HRB1 PE =1 SV = 2 SNZ1_YEAST Pyridoxine biosynthesis SNZ1 Q03148 32 5 3 0.0061980.0025142 2.5 protein SNZ1 OS = Saccharomyces kDa cerevisiae GN = SNZ1PE = 1 SV = 1 RS9A_YEAST 40S ribosomal protein RS9A O13516 22 151 1560.009155 0.0037905 2.4 S9-A OS = Saccharomyces cerevisiae kDa GN = RPS9APE = 1 SV = 3 ARPC2_YEAST Actin-related protein ARPC2 P53731 40 15 70.044768 0.018359 2.4 2/3 complex subunit 2 kDa OS = Saccharomycescerevisiae GN = ARC35 PE = 1 SV = 1 TRS31_YEAST Transport protein TRS31Q03337 32 8 4 0.026095 0.010779 2.4 particle 31 kDa subunit kDa OS =Saccharomyces cerevisiae GN = TRS31 PE = 1 SV = 1 RPA14_YEASTDNA-directed RNA RPA14 P50106 15 7 3 0.036547 0.01524 2.4 polymerase Isubunit RPA14 kDa OS = Saccharomyces cerevisiae GN = RPA14 PE = 1 SV = 1PUT2_YEAST Delta-1-pyrroline-5- PUT2 P07275 64 6 3 0.012072 0.00512562.4 carboxylate dehydrogenase, kDa mitochondrial OS = Saccharomycescerevisiae GN = PUT2 PE = 1 SV = 2 RM51_YEAST 54S ribosomal protein RM51Q06090 16 6 3 0.035158 0.014913 2.4 L51, mitochondrial OS =Saccharomyces kDa cerevisiae GN = MRPL51 PE = 1 SV = 1 LGUL_YEASTLactoylglutathione lyase LGUL P50107 37 5 2 0.012764 0.0053001 2.4 OS =Saccharomyces cerevisiae kDa GN = GLO1 PE = 1 SV = 1 HIS8_YEASTHistidinol-phosphate HIS8 P07172 43 9 5 0.024457 0.010784 2.3aminotransferase OS = Saccharomyces kDa cerevisiae GN = HIS5 PE = 1 SV =2 NPT1_YEAST Nicotinate NPT1 P39683 49 5 2 0.010476 0.0046279 2.3phosphoribosyltransferase kDa OS = Saccharomyces cerevisiae GN = NPT1 PE= 1 SV = 3 METK2_YEAST S-adenosylmethionine METK2 P19358 42 79 750.038801 0.017378 2.2 synthase 2 OS = Saccharomyces kDa cerevisiae GN =SAM2 PE = 1 SV = 3 FMP10_YEAST Uncharacterized FMP10 P40098 28 14 80.055633 0.0252 2.2 mitochondrial membrane protein kDa FMP10 OS =Saccharomyces cerevisiae GN = FMP10 PE = 1 SV = 1 YPT31_YEASTGTP-binding protein YPT31 P38555 24 9 4 0.028763 0.012951 2.2 YPT31/YPT8OS = Saccharomyces (+1) kDa cerevisiae GN = YPT31 PE = 1 SV = 3YMX6_YEAST Uncharacterized protein YMX6 Q04279 106 8 5 0.0073220.0033862 2.2 YMR086W OS = Saccharomyces kDa cerevisiae GN = YMR086W PE= 1 SV = 1 ACPM_YEAST Acyl carrier protein, ACPM P32463 14 8 4 0.0464870.021428 2.2 mitochondrial OS = Saccharomyces kDa cerevisiae GN = ACP1PE = 1 SV = 1 RM33_YEAST 54S ribosomal protein RM33 P20084 10 7 30.054493 0.024282 2.2 L33, mitochondrial OS = Saccharomyces kDacerevisiae GN = MRPL33 PE = 1 SV = 4 RL14A_YEAST 60S ribosomal proteinRL14A P36105 15 111 121 0.010356 0.0050431 2.1 L14-A OS = Saccharomycescerevisiae kDa GN = RPL14A PE = 1 SV = 1 PBP1_YEAST PAB1-binding protein1 PBP1 P53297 79 32 16 0.050084 0.024091 2.1 OS = Saccharomycescerevisiae kDa GN = PBP1 PE = 1 SV = 1 GPDM_YEAST Glycerol-3-phosphateGPDM P32191 72 17 8 0.026484 0.012419 2.1 dehydrogenase, mitochondrialkDa OS = Saccharomyces cerevisiae GN = GUT2 PE = 1 SV = 2 RIB1_YEAST GTPcyclohydrolase-2 RIB1 P38066 38 16 9 0.043642 0.020754 2.1 OS =Saccharomyces cerevisiae kDa GN = RIB1 PE = 1 SV = 2 RSC7_YEASTChromatin structure- RSC7 P32832 50 13 7 0.029347 0.014198 2.1remodeling complex subunit RSC7 kDa OS = Saccharomyces cerevisiae GN =NPL6 PE = 1 SV = 1 OTC_YEAST Ornithine OTC P05150 38 13 6 0.0316970.015373 2.1 carbamoyltransferase OS = Saccharomyces kDa cerevisiae GN =ARG3 PE = 1 SV = 1 UBP6_YEAST Ubiquitin carboxyl- UBP6 P43593 57 9 50.019729 0.0094804 2.1 terminal hydrolase 6 OS = Saccharomyces kDacerevisiae GN = UBP6 PE = 1 SV = 1 SUR7_YEAST Protein SUR7 SUR7 P5400334 8 4 0.021538 0.010088 2.1 OS = Saccharomyces cerevisiae kDa GN = SUR7PE = 1 SV = 1 TWF1_YEAST Twinfilin-1 TWF1 P53250 37 8 4 0.0201410.0093864 2.1 OS = Saccharomyces cerevisiae kDa GN = TWF1 PE = 1 SV = 1RN49_YEAST 54S ribosomal protein RN49 P40858 18 6 3 0.026689 0.0129682.1 L49, mitochondrial OS = Saccharomyces kDa cerevisiae GN = MRPL49 PE= 1 SV = 2 RSM28_YEAST 37S ribosomal protein RSM28 Q03430 41 6 30.014043 0.0067459 2.1 RSM28, mitochondrial kDa OS = Saccharomycescerevisiae GN = RSM28 PE = 1 SV = 2

What is claimed is:
 1. A method of identifying proteins, includingproteins comprising posttranslational modifications, specificallyassociated with a target chromatin in a cell, the method comprising: a)providing: i) a first cell sample wherein the target chromatin is taggedby contacting the target chromatin with a tag capable of specificallyrecognizing and binding one or more portions of the target chromatin andwherein the tag comprises two affinity handles and a nucleic acidcapable of binding a nucleic acid sequence component of the targetchromatin, wherein the nucleic acid sequence component of the chromatinis normally present in the cell, and ii) a second cell sample whereinthe target chromatin is not tagged, wherein the first cell sample andthe second cell sample are lysed; b) performing affinity purification oneach lysed cell sample in (a) using a substrate capable of binding theaffinity handle, wherein affinity purification of the first cell sampleresults in isolation of affinity handle bound to tagged target chromatinand enrichment of the target chromatin relative to affinity purificationof the second cell sample not contacted with the tag; c) identifyingbound proteins from (b); and d) determining the amount of each boundprotein in each cell sample from (b), wherein bound proteins that areenriched in the first cell sample as compared to the second cell sampleare specifically associated with the tagged chromatin in the first cellsample.
 2. The method of claim 1, wherein the nucleic acid capable ofbinding a nucleic acid sequence component of the target chromatin is aguide RNA (gRNA).
 3. The method of claim 1, wherein one of the twoaffinity handles is a nuclease inactivated Cas9 protein, or derivativethereof.
 4. The method of claim 1, wherein one of the two affinityhandles is Protein A.
 5. The method of claim 1, wherein the targetchromatin in the first cell sample is tagged by expressing in a cell atag comprising a nucleic acid capable of binding a nucleic acid sequencecomponent of the target chromatin.
 6. The method of claim 5, wherein thenucleic acid capable of binding a nucleic acid sequence component of thetarget chromatin is a guide RNA.
 7. The method of claim 1, wherein thetarget chromatin is tagged by expressing in a cell a gRNA capable ofbinding a nucleic acid sequence component of the target chromatin, anuclease inactivated Cas9 protein that associates with the gRNA, andProtein A.
 8. The method of claim 1, wherein the second cell sample isnot tagged by contacting the target chromatin with a non-functional tagthat is not capable of binding a nucleic acid sequence component of thetarget chromatin and wherein the non-functional tag comprises twoaffinity handles.
 9. The method of claim 8, wherein the second cellsample is contacted with a non-functional tag by expressing in a celltwo affinity handles, wherein the nucleic acid capable of binding anucleic acid sequence component of the target chromatin is not expressedin the cell.
 10. The method of claim 1, wherein the chromatin isfragmented to comprise nucleic acid sections comprising 500 to 1500 basepairs.
 11. The method of claim 1, wherein the target chromatin in thefirst cell sample is contacted with a tag during cell culture and thetarget chromatin in the second cell sample is contacted with anon-functional tag during cell culture.
 12. The method of claim 1,wherein the target chromatin in the first cell sample is contacted witha tag following cell lysis and the target chromatin in the second cellsample is contacted with a non-functional tag following cell lysis. 13.The method of claim 1, wherein the first and second cell samples arebiological samples.
 14. The method of claim 1, wherein the first cellsample and the second cell sample are crosslinked and then lysed. 15.The method of claim 1, wherein the identifying of step (c) involves massspectrometry.
 16. The method of claim 1, wherein step (d) involveslabel-free proteomics
 17. The method of claim 16, wherein the label-freeproteomics technique is spectral counting.
 18. The method of claim 1,wherein proteins enriched in the first cell sample compared to thesecond cell sample are enriched by at least 2 fold.